The limit is Storyguide fiat - what rewards you get from twilight are entirely up to the SG(1)
It is entirely possible to get a 2nd Major Hermetic virtue. The description for magical focus says you can only have one magical focus, regardless of source, so under the rules "as written" you shouldn't get a second magical focus.
(1)I have seen the virtue "Twilight Mastery" in Guardians of the Forests. We once let a Criamon take it. Never again. In the hands of a non-munchkin player whose character doesn't have Twilight Prone this may have been a sensible Major Virtue, but it's too abusable.
I was afraid of that.
So much for trying to argue that the Tremere will gain a Minor Magical Focus in Winds after botching diverting the accursed gale.
EDIT: Rereading this, I guess I am still processing the big revelation of the night, as I should have written "Mythic blooded Merinita", not "Tremere".
We all knew that our troupe's Merinita character had Strong Faerie Blood and Mythic Blood, and that the SG had allowed a couple of extra weeks for the player to decide which Faerie Blood and which Mythic Blood. We just found out it is Dhampir and Tremere's blood.
This is known to the players, not our characters. My Tremere character can't act on this information. This seems to be weighing on my mind somewhat.
Is it possible to get a totally new Hermetic/Supernatural virtue by this good Twilight Experience?
That is, if the circumstances/story were appropriate.
A hypothetical example might be examining a Ancient Magic type device, and Twilight lets you learn the forgotten Virtue of creating that device?
Or another hypothetical example is you go into Twilight while being cursed with some exotic magic, you gain a never before seen Virtue related to negating, surviving or controlling that magic.
Not only is it possible, it's probably how a good portion of the Hermetic virtues and flaws came into being in the first place - people trying to use their magic and experiencing strange twilight effects getting these virtues and flaws, and then their apprentice may pick up some of their parens' quirks (if you use the rules from Apprentices), and eventually they spread out among a Hermetic House from an early member's experience.
Gaining a "totally new" Hermetic/Supernatural virtue from Twilight is certainly possible. In fact, at our gaming table we probably see more "new" than "standard" Virtues gained from Twilight. It's even in the spirit of Ars Magica: in older editions, Twilight often allowed a magus to gain an "improved understanding" of the Arts, allowing him to write higher level books.
All the examples you give seem very reasonable. The only caveat when designing new Virtues is that they did not get playtested, and they might interact in unforeseen way with the other mechanical aspects of Ars Magica. But even then, if you have to introduce a new Virtue, introducing it through Twilight is one of the best ways: if you find you have to "tweak it" later in the game to preserve game balance, you can explain the change far more easily ("your magus had not completely recovered from his experience, so ...") than with Virtues introduced through other means.
We have always house-ruled that the Tremere virtue was not a focus, but "certaman training", thus allowing them to get a focus. Then again in several years of laying this game regularly I think Certaman came up... Three times? So the Tremere virtue was severely underpowered.
It occurs to me that this may interact with the breakthrough rules.
The researcher is plugging away gaining breakthrough points, suffers Twilight in the process but gets a good result, and thus immediately learns the "virtue" he was aiming for.
But would this give full understanding, or merely mean the researcher is now a source of inspiration for himself?
Note that which virtue the researcher gains depends on the decision of the troupe. It's certainly very fitting that the magus might gain the virtue he was after -- but not necessary. Also, keep in mind that gaining a virtue through Twilight is not quite the same as gaining it through a breakthrough in terms of being able to teach it to others.
In the French rulebook they say you can pick any "Vertu mystique" which could be translated to "mystic virtue", which doesn't exist.
I assume that term encompasses all Supernatural and Hermetic virtues.
Same for flaws.