Also, when you think about it, if a game behaves differently when run in an emulator, as part of an emulator-and-ROM bundled software product released by Nintendo... then that behavior is just how that particular release of the game has been canonically chosen to behave. Any bugs in the emulation of a Virtual Console title, or a SNES Classic title, or a SNES Online title, are just "how that version of the game is." Much like any typos in a particular printing of a book are "just how that release of the book is." They're now part of the authorial intent of that release; part of the text. If you later ported that game, you'd seek to be bug-for-bug compatible with the bugs introduced by that emulator, because those bugs are what Nintendo released, and so those bugs are now, in part, what it means to play that game.

Or, to put that another way: there's no real difference between a bug introduced by wrapping a game in an imperfect emulator, and a bug introduced during recompilation/porting/remastering of the game. Either way, you now have a new "variant" of the game with its own bugs, but one which is also a canonical, supported release of the game.

Interestingly, sometimes—because of one of these slight variances—the fastest [and so preferred] version of a game to speedrun, is a Nintendo-sanctioned emulated (e.g. Virtual Console) release of the game. It says something important, I think, that these releases of the game aren't automatically shunned by the speedrunning community, the way that runs of the game under an arbitrary emulator on someone's PC would be; but rather are just treated as their own separate category-set, in the same way the speedrunning community differentiates different region releases, or version releases, or port/remaster releases.