Okay, here's some more info about the issue (insofar as there is an issue).
What SCS does is look at every creature that's using a "standard" combat script (wtasight, mage18a, etc.) and change its spell choice and scripts (and occasionally level, where there's a big discrepancy between level as indicated by spells memorised and as indicated by actual level).
What I normally say to modders who want to insulate their creatures from SCS is: use a bespoke script. (Use an unmodified copy with a new name, if you prefer.) For most people it tends to be the other way around: they actively prefer SCS AI to apply to their creatures, usually because they don't want to write their own AI and would rather use whatever the background one is (whether SCS or vanilla).
However, SCS doesn't check for area-assigned scripts, mostly for pragmatic reasons (I'm lazy and it's hardly ever used in the BG-series games). Nothing terrible will happen as a consequence (the creatures will get a few spells they can't use).
Here's my advice:
(i) If you actively want SCS not to affect these creatures for whatever reason, and you are using bespoke creatures that don't get reused elsewhere in the game, just wipe their cre-file combat scripts and let the ARE file handle it.
(ii) If you're happy for SCS to affect the creatures, and again you're using bespoke creatures, assign the scripts via the cre file rather than the are file.
(iii) If in either case you're using non-bespoke creatures, make unmodified copies and use them instead. (That would be my general advice in BG and BG2 anyway - the IWD method of assigning all scripts by ARE file is in many ways more elegant, but BG2 is so thoroughly committed to the cre-file model that occasional deviations from it probably cause more confusion than they avert.)