I'm not convinced CloneCD is appropriate for Sega CD / Saturn games, or even bin/cue's in general.
The last time I did a series of ripping tests, CloneCD stuck an extra sector in the binary (.img) somewhere, and I think the rest of the sectors in the bin were then offset by one spot. I don't remember this happening in previous tests I did with other titles, so it makes me wonder what's happening there. It could just be a fluke in this most recent case.
CloneCD also seems to do a half assed job with cuesheets in general. While every other bin/cue ripper I can think of right now marks a new track with both "index 00" and "index 01" lines, CloneCD skips the "index 00" line altogether. I seem to remember having problems loading the cuesheet into a burning program, but I can't say for sure right now. While I don't think this is technically correct, I would rather use something that I know is reliable.
So right now, I'm not going to say CloneCD does or does not work well for what you want to do, I would suggest exploring other options first.
btw, why can't you use CDRWin?