Yes, there are a number of potential pitfalls here. As I think Ivo alluded to, your jpeg isn't really doing what I think you think it is doing. It will be demosaiced and interpolated into what it thinks is RGB, despite the missing matrix. The red cast, well, who knows how that came about, even if the UV-IR cut is now missing, and you found a way to "white balance" things into gray submission. The good news is that you haven't yet seen the crisp resolution increase that you should obtain from your mono mod!
Unfortunately, DSS will force debayer anything in a RAW format, you cannot turn it off. You can do so with FITS files. I am unsure if any acquisition programs will write out FITS from a DSLR, however. As far as I know NINA will save RAW files (NEF, CR2, etc) from DSLR despite having the program options set to 16-bit FITS.
Freddy, an ST-user and member here, also has a mono modded Canon. At first he was using dcraw to batch process his CR2's by saving them as TIFF using a special command line option for no interpolation. Ultimately he gave up on that and now uses PI for his stacking, as it has an option for no debayer/interpolation of RAW files.
I believe I tried ASTAP on some of Freddy's sample mono CR2's, and that didn't work out either, even though I thought it might. But ASTAP is updated frequently, so might be worth a look to see if anything has changed.
Another potential issue is just what the "black box" of Canon RAW pre-processing is doing. In many cases, nobody knows, unless they can reverse it out and come to conclusions via experimentation. That's how things like Nikon's lossy compression bucketing were found out, and a fix devised. But other things are done to massage RAW files such that they aren't really, fully, RAW, like you'd probably get from an astrocam. Thus, it's possible that you might have the pixels for your red and blue "channels" increased, even though the matrix is now gone, if Canon does that sort of thing.
It might be worth looking around to see if those who currently use mono mod Canons are also implementing some kind of replacement firmware hack which eliminates any such problems, or at least confirm whether or not it is something you need to worry about.
It may very well become apparent visually when you get your first looks at one of your mono CR2's.
Let us know what you find out -- it does seem very interesting!