According to the CloneCD Hardware Requirements (why doesn't anybody check this ? ) the drive has the following features:
Yamaha scsi 8424 :
WRITE MODE: RAW-SAO
READ MODE DATA: RAW+96
READ MODE AUDIO: RAW+96
The Yamaha IDE 2216 isn't mentioned
But to answer your question if you can back-up Red Alert 2, the answer is NO. RA2 has the SafeDisc 2 protection and Yammie's can't handle this...