As I mentioned in the other thread ... you will have to Debayer NO MATTER WHAT if you're capturing saving as FIT. It doesn't matter if we DISPLAY the image as color...the actual FITs files will have to be Debayered...it's just a fact of life as FIT data is almost always 16BPP (16 bits per pixel grayscale). I can guarantee you if you hand me a FIT file that came from APT or SharpCap it will be 16BPP and grayscale. Just because they debayer for display means nothing about how the data is saved.
If you don't want to deal with debayering then I suggest you capture as CR2 if shooting with a Canon or NEF if shooting with a Nikon. Both of those are available for their respective DSLRs in the Settings for those cameras.
We do CAPTURE color compatible images (to the standard FITs specification), we just don't DISPLAY in RBG.
Hope that helps,