I was always super confused when working with color SER files in Siril. In particular, the program always says you can “debayer them on the fly,” but I could never figure out how to do that. The files are definitely beneficial when doing lunar or planetary work, as they are processed much faster by Siril than hundreds or thousands of FITS files. But registration and stacking wouldn’t work if they stayed mono the entire time.
But I found the trick! In the “Conversion” tab, make sure the “Debayer” checkbox is checked. You may also need to ensure your Bayer matrix settings are correct.
Load your SER file as a sequence in the “Sequence” tab.
Now your sequence will be debayered and ready for registration and stacking.