It`s because VC and EMU give an unfair advantage to the original N64 platform due to having little to no lag on EMU (depending on your settings) and EMU having no lag at all. Plus it's easier to cheat on EMU and VC as proved by Mario 64 speedrunning history. There may be other reasons that I may not be aware of, but that should be the gist of it.

I don't run on Emulator or VC anymore and haven't for a long while. My take though is that runs on Emulator and VC for Stage RTA should be fine for certain stages. Splitting the leaderboards for Emulator and VC already neutralizes most of those runs anyways. Not for a bad reason. We could always just separate those leaderboards too. Regardless of that though. If it never did change which I would completely understand. I'd suggest getting on the Ultimate Star Spreadsheet and using that for your Stage RTAs instead. The spreadsheet is for recording your own times and isn't moderated by anyone unless you are trolling or have a record for a star that wasn't gotten on N64.

As for my answer to Kulty. I think you're right completely. It is easier to cheat on Emulator. It's not easier to cheat on VC though. That's not why there are not separate leaderboards for Stage RTA. It's just because of the community legacy I feel. It's much easier to set a World Record on Stage RTA or Single Star using VC or Emu advantage instead of N64. Since historically we haven't had a faster time than N64 on VC or Emulator for years and considering that VC and Emulator are not as competitive. It would create a lot of controversies if we had separate leaderboards but all the faster Single Star and Stage RTA times were on other platforms. It would devalue N64 times slightly. This is why in 120 Star when someone on VC got the WR and beat Siglemic. Siglemic immediately struck back with a run posted in shit quality with worse gameplay than the N64 World Record but was still faster than Hyassin's time as well as his own N64 World Record. Siglemic was trying to tell us that beating a record because version differences didn't necessarily mean the record was better. Hyassin never cheated, it's just that his run wouldn't have been World Record if performed on N64. That was also the last real World Record ever performed on Virtual console which was years ago.

Stage RTA is already very underplayed, vc/emu would be graveyards and serve no purpose to highlight any sort of "competition". For the most part ppl doing stage RTA are doing it to practice for normal RTA and we already have a sheet for tracking that sort of stuff.