I have a question about this. I know for bonus equivalent special abilities you subtract the enhancement bonus from your total attunement bonus to determine your final enhancement bonus. What about special abilities with a flat gold cost, like adaptive or glamered? Do those count as part of the attunement bonus as well, or are they separate?
They don't interfere at all with attunemet.
As a fan of ABP, I recommend you to read this blogpost. It contains an addition to the attunement rules. The math looks a bit intimidating, but in my experience it's overcomeable and really improves one of the glaring weaknesses of the conceptually fantastic ABP system.