As always, Nintendo really doesn't like people playing their games or using their hardware in ways not intended. Anything that lets people "break" the game by playing in ways not intended Nintendo considers a bug. It doesn't matter what it is, could be as simple as changing/removing mechanics in Mario Maker people relied on as part of the core behavior and breaking a lot of things that were possible to do in Mario Maker 1 (with no downsides simply extending the base functionality with extra features that were only possible because those quirks existed) in the sequel. Making the removal of the online services in Mario Maker 1 a lot more significant than it would otherwise be. You have no way to transfer the stages because they just don't work in 2, and any of those unique stages are forever lost to the times now that the online services are removed, you can't share them anymore...
Something like the Backwards Long Jump in SM64 would just not happen nowadays because they would never let a bug like that slip that would allow you to skip parts of the game nowadays. That's unintended and therefore bad. They even took the trouble to patch it out of the Switch Super Mario 3D All-Stars release. Something that nobody would ever know or care is there unless they were actively using it so it's not like you can argue that leaving the bug in was leading to a lesser experience for legitimate players.
Like it or not, the BLJ has become such an integral part of SM64 history, removing it now is like releasing a port/re-release of a game but purposely changing the game in basic ways to make it different from how the original plays. Nobody wants that, they want the same old game they know and love.