If you take your character from BG1 into BG2, you do get 6 innate abilities--but you might not get the same ones. Which ones you get is determined by your character's ALIGNMENT, not what your Rep. was during BG1. Only Lawful Good and Neutral Good characters get all 6 Abilities earned through the Good path (Cure Light*2, Slow Poison*2, Holy Might*2), and I think only Chaotic Evil characters get all 6 Evil abilities. All other alignments get their own mixture of Good & Evil.
If you want to use Shadowkeeper to edit your Special Abilities to what they were at the end of BG1, I don't think anyone but an ironclad purist would have a problem with that.....or you could plan your BG1 character's alignment to make sure you get the Abilities you want in BG2.