You will not be able to retroactively choose special abilities for any levels gained as a result of removing the SoA cap. You will only get to choose abilities for levels gained after you install ToB.
For example, fighters should begin getting special abilities at Level 20. If you remove the SoA cap and get to level 23, and then you install ToB, you will only get to choose an ability once you get to level 24 - it doesn't allow you to retroactively choose abilities from levels 20, 21, 22 and 23.
It pays to not remove the cap. Better to get ToB if you're planning to play it.
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