I don't know if there are native tools to write CDI images, but I just tried the demo of Disc Juggler 6 under wine and having it read from a Saturn image mounted via cdemu and it seemed to work fine without having to do anything special.
Ok, thanks, I did get cdemu installed. I was looking for a batch processing solution. So with cdemu, I just need a way to rip the virtual image to CDI format via bash script. I don't think Disc Juggler 6 could do that.
I don't think there are any options for that on linux without rolling your own, you might be able to do something like use binchunker and a modified MDS4DC. MDS4DC is a dreamcast MDS/MDI creator that has a linux compatible fork floating around, so it's not compatible out of the box; From a cursory look it might work for single data track images and single data track images + cdda if you remove the self-boot check before compiling. From the looks of it, it does not support multiple data tracks (like NiGHTS has) out of the box either.
I don't have a Rhea/Phoebe (wish I did) so I couldn't test if I wanted to.
I made a quick fork w/ that selfboot test disabled, unfortunately the "l33t-speak" is still there. I wouldn't keep your hopes up, but it could be a base to start on if nothing else. I know there are people in the community that have already done the brunt of the conversion work from redumps -> ccd (might be cdi), so honestly that might be the quickest solution...