I made a topic on this website a few years ago about changing the Sonic CD soundtrack in Sonic Gems Collection for PS2. Having revisited my own steps and doing some new research on the matter when trying to run my old ISO on real hardware, it seems that there are a few things I should've been more clear on the last time:
I'm only linking to my blog because I don't feel like re-formatting the article for a quote box. The information is anyone's for the taking, and I encourage the talent of this website to add to it in any significant way they can! There's something in me that wants to swap out a few of the roms found in Gems for some of the Mega Collection roms to make the best re-hashed compilation of Sonic compilations that's ever graced 6th-gen platforms (well, either that or disable the time limit in the demo roms). :P
Looking at the code of the master ISO, it also looks like several parts of Sonic CD load like executables too (considering it was a PC port, at least).
Good luck to anyone that might actually go to the extent of modifying and repacking soniccdu.cvm! I haven't tested this in years, but as far as I know, it shouldn't be too difficult to circumvent write-protection and data padding for both GC and PS2 at this point. You guys probably know more about that than I do!