QUOTE
Such a character will not have as many adept powers as most other adepts, nor will they be able to cast spells with the same skill as true magicians.
Seems to say right there that you don't use your "full" magic rating when you're casting spells, just the amount of magic that your mage side has been allocated, otherwise you'd be casting with the same skill as true magicians.
Perhaps there was some concern about mystic adepts doing the following...
(this is from my looking over the adept power right now, so it's not even close to an exhaustive list of how mystic adepts might be broken)
Attribute Boost. Allocate just a single magic point to being an adept and you're suddenly rolling 7 dice to see how much to boost Strength, Body, Reaction, Agility, all for twice as many combat turns as successes generated. "Free" attribute boosts?
Enhanced Perception. For mage faces, spend a single magic point for four levels and suddenly you're +4 dice for every assensing test and the loss of one die probably won't hurt for all your mystic mind control spells.
Improved Ability. Same as above, lose one magic point for a +4 dice bonus to a non-combat skill.
Kinesics. Face mages again, lose 1 magic point to get +2 dice to all social skills
Mystic Armour. Lose one point of magic to get a permanent 2 points of armour that work against everything and that doesn't use up a precious focus (focus addiction is bogus -- what other class, other than technomancers, has an addiction chance for doing what they do, but I digress)
Rapid Healing. Lose 1 point of magic and gain 4 dice to natural healing test -- just take the drain, then shrug it off.
Rapid Healing -- this change also stops people who buy combat reflexes 3 and then 8 levels of rapid healing with their remaining two points. Now you have to spend a magic point on spells, and also buy killing hands instead, darn.
And that's just looking through SR4A just now -- I didn't even touch Street Magic. These seem like a nobrainer to me, which means they're probably broken. The FAQ change really seems to balance things out. I think every GM should go by what the FAQ says about Mystic Adepts.