Actually ATAPI was originally made for SCSI and they just ported it to IDE, that's why it is practically same. I think those checks are just to make sure everything is ok and you can propably just ignore them. Also Sunrise IDE BIOS is originated from earlyer SCSI bios, so that should be quite similar as well. Unfortunately I don't have experience of programming SCSI CD... I think that long time ago I made some program to eject CD, but this does not really help.
The feeling that I have is, that SCSI devices are generally much more independent than IDE devices. You can for example let the harddisks copy stuff between them without bothering MSX at all. How ever this makes it nessessary to check what has been done in order to know if commands are implemented already. Maybe this is the reason you can see so many checks?
This is anyway pure speculation... Anyway good luck! I like the idea of SCSI support a lot!