shoot, i forgot that PI does not use dcraw anymore to import CR2 files.
honestly juan might have to answer this question. i looked thru the source code for the RAW file handler and i'm not totally sure how it interfaces with libRaw - i don't know what libRaw is going to do if you ask for CFA but also ask for a white balance to be applied. the answer is not in PI's source code.
i suppose you can find out if this works by setting some really extreme custom WB (like on an orange card) and then opening an image with and without that custom WB and see if you get something different when you debayer the CFA image PI gives you...
at any rate, usually the answer to this question is that you don't want/need to bother with custom white balances when using a DSLR for astrophotography but of course you might have some reason for wanting to do this.
rob