Sahir (which is what I'm particularly interested in here, although the general case is useful as well) say that:
I suspect that in practice that's what's going on for all the traditions, but it's just worded with differing degrees of care in different places. [Actually, my feeling is that what would make sense is to create a new version of "Hermetic" for every hedge tradition, rather than just use "Supernatural" for them, but that doesn't seem to be what the books do.]
I think Greater Magical Defenses wouldn't affect the addition to Magic Resistance Forms give (as the virtue explicitly says "if a hedge wizard acquires a Magic Resistance (he acquires Parma Magica, for example), it is not affected by this Virtue". Things like bonuses to soak from the Forms seem like fair game, though.
I'd be tempted to treat separate traditions almost like separate characters.
Your access to both is being paid for by the amount of extra study that a second tradition requires.
Your virtues/flaws need to balance out when considering the character within each tradition, independently from the other.
This makes the question of whether a virtue/flaw applies to both traditions a character design choice rather than a ruling.
You can't take extra flaws in one tradition to compensate for another's extra virtues
e.g.
Generic Virtues: +5
Generic Flaws: -6
Hermetic Virtues: +5
Hermetic Flaws: -4
Alternative tradition Virtues: +5
Alternative tradition Flaws: -4
I think that's the same as what I proposed earlier? By which I mean "I think that's a sensible idea", but it didn't seem to get much of a response earlier.
More seriously, unless someone points out a significant problem with it, I'd be inclined to House Rule that way instead of going for "your second tradition is entirely vanilla unless you've got room in your standard +-10" or "all of your Hermetic virtues and flaws automatically apply". The vanilla tradition member approach is probably the canon, though.