As far as I know, the intention is was for Favoured Abilities/Arts to work the same everywhere. If the rules are apparently different in different places it is (I think) merely a mistake and comes down to different authors writing different things and mis-understanding the others.
The version that I prefer is that in Hedge Magic. There the rule is that:
When you learn a Favoured Supernatural Ability/Art for the first time you suffer no penalty to your Study Total (due to existing Supernatural Abilities and Art Scores.
When you learn a non-Favoured Supernatural Ability/Art for the first time, you suffer a penalty to your Study Total (based on all of your existing Supernatural Abilities and Art Scores; including favoured ones).
If you already have a Score in the Supernatural Ability/Art, then your Study Total is not penalized at all.
In this system, the Hermetic Arts are effectively the favoured Arts of The Order of Hermes.
Other people may have different preferences, but for my money that is the easiest and simplest set of rules to understand.
Disclaimer: Of course, I wrote the version in Hedge Magic, so I would think that. I wasn't intending to write something different to the other cases, and I thought that I had modelled my wording from that in one of the other books (probably ROP:Divine).