You're right. If you got to ignore them then other supernatural abilities get to be "almost-favored" by extension.
That was one of the ambiguous issues in this thread. Different books apparently handle it differently. Erik Dahl suggested that Favored Abilities not penalize the learning of other Supernatural Abilities. On the other hand, Richard Love said his preferred version was that they do penalize normally.
That's the way it is in RoP: Infernal, and I suggest doing it that way for Divine and Faerie Abilities too. (Magic ones work differently, because they're tied to Opening the Arts, so I really think of them as a different mechanic.)
The rationale for my suggesting the Infernal mechanic is that if it doesn't work this way, it is kind of dumb for a player to take any of the character's Favored Abilities as Virtues. The clever thing to do would be take a bunch of Supernatural Abilities at character creation that are not part of the tradition you are planning for the character to join, because they won't affect your study total when you learn its Favored Abilities. If Favored Abilities also don't subtract from your study total for learning Divine and Faerie Abilities, there is less incentive not to take them early on, since theoretically they don't affect your chances of learning others and you have a larger pool of experience points to spend on them.
No. But the character can belong to a tradition that favors it; that's up to the players.
In my experience, most players prefer that the Ability is not Favored, because there's no benefit once you have the Ability, and in fact it limits your options a little because that's one less Favored Ability you can learn.
I would say it's irrelevant.
Being Favoured lets you learn the Ability without penalty to the Source Total, when you have no Score in the Ability. Having the Virtue gives you a Score of 1 in the Ability, so you won't be penalized for subsequent learning anyway.
Unless you are using the apparent definition of Favoured Ability in ROP:Infernal, then it is apparently relevant. Although I don't really understand why ROP:Infernal has a different definition to ROP:Divine, ROP:Faerie and Hedge Magic.
Absolutely. That is the point of Favoured Abilities mechanic.
You aren't meant to take your Favoured Abilities as Virtues, and this frees up your Virtue slots for something else (which could be different Supernatural Virtues, if you want). If this wasn't the case, every character from the tradition will look practically exactly the same (from a Virtues perspective), because they will need to take the five or ten (or whatever) Virtues needed for the tradition's Supernatural Abilities/Arts.
Assuming that the character creation process is agnostic about how and why a character acquired his Virtues (which it pretty much is).
However, this doesn't change under the ROP:Infernal version. You are still better off from a game-mechanics perspective to take non-Favoured Supernatural Abilities as Virtues during character creation, rather than try to learn them during play. This is because during play (presumably) it is hard to find someone who will teach the Supernatural Arts/Abilities of a foreign tradition, and also because even if you can find a teacher/book, learning non-Favoured Supernatural Abilities are still penalized (even under the apparent ROP:Infernal rules) by the other non-Favoured Supernatural Arts/Abilities you have.
While that makes perfect sense from the perspective of game balance, the logic from an in-game perspective is a touch... weird,
As an occasional GM I would be more inclined to make the members of traditions extremely suspicious of folks with other powers (just because a player wants to join the Witches of Thessaly doesn't mean that he/she will find a witch willing to let them in, and if they display powers that are linked to another tradition then they might have good reasons to be extremely cagey with their secrets with someone they feel might be trying to infiltrate their order),
Then again, I suppose the same logic could be applied to not gaining further benefits for joining multiple traditions... Maybe what traditions need is a big sign-up penalty (an initiation ceremony to join granting the virtue: "Tradition: Whatever" which grants the favoured abilities, but also some flaws that make the players wary of joining multiple traditions...),
Both of these need be addressed by the SG, separating the Player from the Character in terms of the eventual Story and addressing each realistically in terms of either successful meta-play or achieving a successful IC story arc.
For the first, if a Player wants to tell the Story of a Character who joins the Witches of Thessaly, then the SG should either respect that Player's wishes, or admit that they believe in an adversarial "Player vs. Dungeon Master" sort of dynamic, where the DM's job is to make life as difficult as possible for the Characters. (I don't believe that's so, after a point.) Challenges, sure - but everyone needs to have Fun, and simply making a decision or rolling a die and saying "Nope, you're screwed" is not the path to that fun for that Player.*
So, for that, the balance is between the SG maintaining a reasonable presence of difficulty (or suspension of belief in the inevitable success) and simply giving it away.
(* Some Players would be happy perpetually trying to join the Witches - that's different, and not what we're talking about. Otoh, for a Player who wants to start a Character in several Traditions and then join the Witches, we move on to the next point...)
For the second, there is an existing in-game mechanic for not joining multiple traditions - and that's the first Traditions themselves. Some but certainly not all traditions would tolerate such a diverse display of interest - if you are interested in the Witches o' T, then those are who you are expected to be loyal to, and then running off and also trying to join some other group might be seen as either abusive to their trust or treacherous to their secrets. (Likewise, having previously belonged to one Tradition could easily be seen as a dealbreaker for any second - either the prospect's motives and loyalties are suspicious, or (if they quit the first) their dedication and commitment certainly is). Traditions are not commodities that one can simply pick off a shelf, or at least they don't see themselves as such - there are, IC, very real reasons why one is accepted and another is not, and loyalty and dedication are going to be primary among those for many, if not all.
And here, the SG's job (in the absence of Player awareness of the fact) is to make such Players acutely conscious of the fact that a Tradition is not simply something you sign up for one summer and then move on to the next, and again and so on, like hobbies or summer sports leagues - or at least, not necessarily so (some trivial ones might be, depending on their nature and membership expectations).
Fair point, let me agree by suggesting a slightly different approach...
If a player wants to "tell the Story of a Character who joins the Witches of Thessaly" then maybe at character generation time the GM should be encouraging the player to take virtues for one or two of their favoured abilities (as well as other appropriate abilities, personality traits, etc), and thereby create a character (and not just a player) with the interest (and ability) to join the Witches (I seem to recall the witches are a bad example because it is possible to be an Ex Miscellanea Witch of Thessaly, but stick with it...),
It could be argued that if a player telling you his character wants to join the Witches, while his character seems totally unsuited to that tradition, he is perhaps saying "my character wants this, but he isn't very good at it, so it will be a real struggle - maybe even impossible, and possibly the theme for my characters entire story - only achieving success at the climax of the campaign", while a character built with those perks built in is saying "my character is like this - perfectly suited to joining the witches, so signing up should not be a serious problem",
Under those circumstances (and perhaps in discussion with the player), it is highly appropriate to make signing up a challenge (not impossible, and I apologise if I inferred that, but a serious challenge (and not that big of one when you consider how effective Mentem magic can be!)),
No apology necessary, and, absolutely, this sort of negotation/dialogue between SG and Player is best conducted before CharGen, even before the game is confirmed. (Elsewhere I've suggested that any Player should make sure that this SG is going to run the sort of game they enjoy (esp in PbP!), and both should make sure that a Character is approp for the type of game the SG will be running.)
Challenges are always appropriate, for Players to seek or invent and assign themselves as well those the SG introduces - if the entire story were a cakewalk to where ever the PC's wanted to go... well, it would not be "my" favorite pawn of vis, that's fer sure. 