What I think really happened is that they originally planned on it being backwards compatible, but then realized how many games depended on undocumented opcodes and bugs that had been 'fixed' in the 6502 mode of the 65816. At that point, go back to your bread boards and go nuts removing anything that was there for NES compat but was holding back the SNES in some way. A few iterations of that and you have a pretty much what an SNES was on launch.

Edit: Thinking about it more, that all would also make sense given their strategy past the SNES for back compat. On the GBA they literally just have a complete GameBoy SoC on the die. It's not accessible to GBA software, is probably clock gated in GBA mode, but is there with as few changes as possible from GB hardware to run GB software. Then for the Wii, the companion ARM processor (Starlet as it's known by the Wii hackers) will go so far as to patch problematic GameCube games on load even though it's very nearly identical hardware with a few extensions. It seems like they either drop down gate for gate compat, leave a back door for themselves to get really dirty with patching, or these days just keep an emulator around that they've re-QAed each game on that they'll allow. They're very intentional with back compat in a way that feels like an ancient learned lesson internalized by the company.