I don't know if you're writing your own dev stuff for CD, but there's a few cool things you can do with the PCE CD format.
While the syscard doesn't support ISO-9660 format, you can make such formatted/layout discs boot on the system. The system card only cares what index 01 is in terms of LBA (index 01 is the end of the pre-gap and the start of the track). You can align it to something specifically fixed in a real ISO (a file) to boot from.
Or, you can exploit a trick defined way back.. that the first track can have a near infinite size pregap definition (some professional companies hidden music tracks in the pregap like this, so you had to 'rewind' into it in order to hear it). The system always looks for index 01, of any track (data). So you can hide an ISO binary inside the pregap area, and have the PCE code after that. Both PCs and SegaCD, use a hard coded offset that's equivalent to a 2 second pregap. I say equivalent, because it uses the LBA instead of "indexes". I was able to make a dual boot SegaCD/PCE-CD disc this way.
But yeah, both ways work. The second method means you can't access the ISO binary though, even if it is on the same data track. The first method means you can, but if you want to actually handle parsing the CDFS table - you'll have to write that code yourself.