Yeah, I kinda figured it would be better in native mode, but I wasn't clear if there would be 6502 instructions are can only be used in emulation mode, that's what I mean to ask in my above post.

"Hence why you see the CLC/XCE right off the bat at the beginning of SNES titles. The 65816 starts in emulation mode, hence why this is necessary."

Yes, I've seen that before in all the titles I've disasembled, the CLC/XCE is like the very first 2 lines or very near to that in all of the roms I've looked at.