Guilty as charged, sorry: I do touch CRE files. Specifically, I touch the CRE files of any creature which uses one of a (long) range of core-game scripts. So if you give your custom mage a standard mage script like MAGE18A.BCS, SCSII will change the creature file in two ways:
(i) if the level is too low for the memorised spells, it'll be changed.
(ii) the list of memorised spells will be rearranged (somewhat-at-random) to give a set of spells more optimised for SCSII's scripts.
I don't do anything more drastic than that: if you create a by-the-book 17th level mage, for instance, SCSII won't touch his level. The only reason I muck with level is because the vanilla game has lots of enemies with 9th level spells flagged as L10 (for instance).
If you want to mark a creature as hands-off for SCSII, the easiest way is not to use a vanilla-game script. Even if you don't want to write your own, you could just make a copy of a vanilla-game script and give it a custom name.
I only touch mages and priests, though: fighter HLAs are assigned at script level if you're high enough level. From the next release I'll probably mark this so it only happens in ToB and WK.