Since posting checked SD wiki https://en.wikipedia.org/wiki/Secure_Digital and found "Risks of reformatting Reformatting an SD card with a different file system, or even with the same one, may make the card slower, or shorten its lifespan.
Personally, I wouldn't worry about stuff like this unless you encounter a specific problem. It is true SD cards contain controller and firmware which can behave unpredictably if not used as the manufacturer expected, but this is totally undocumented and is likely to vary from card to card. Even different production batches of cards of same brand, capacity and model could use entirely different firmware, controllers or flash chips.
In the real world, people reformat cards and they continue to work fine. Chances are the designers worked to make it function correctly when formatted by typical devices like cameras or PCs. It is conceivable that things like partitioning, or formatting a card that came exFAT as FAT32 will cause some card to behave badly, but there's no way to know without careful testing of the particular cards.
If you want to minimize the chance of running into problems, your best bet is to stay as close as possible to "typical" users usage. So my advice is find some decent name brand 32 GB cards on sale on newegg or amazon or wherever you buy stuff like that, dedicate some of them to your CHDK camera and some to your Nikon don't worry about it.