here's the scoop...
there is OS 9.....& there is OS X....too completely different systems as u can see...as well as Photoshop 6 & 7 are coded differently...
many applications are having to be rewritten because they are meant to work in OS 9 not X (X isn't traditional "Mac OS"...is actually Unix tweaked out to work on Macs)
the way this works is when an application is "X compatible"....it has the ability to run in either OS (9 or X)....but it's not backwards compatible with older versions of software....kinda like u can open a Freehand 8 file in Freehand 9....but u cannot open a Freehand 9 file in Freehand 8....makes sense so far?
anyway....OS 9 works independently.....while Classic Mode works while running OS X...in which case u are having one OS control another OS (kinda like on a pc DOS with Windows)...
the main difference between running Photoshop 6 in OS 9 & running it in Classic through X is a performance downgrade.....simply because u have OS X controlling OS 9 controlling Photoshop 6...
if u had Photoshop 7.....u could run it natively on X....or natively on 9....it's built to work on either system.....where Photoshop 6 only works natively on 9...
did I confuse u any? it's kinda late and I'm most likely not explaining this too well....but hopefully if I miss any key points here someone will pick up the pieces for me....