I think the taskbar rule should be removed so you're required to show your mouse via webcam. Currently the rule is to show your taskbar OR show that you're clearly clicking the mouse. Using a background program can be easy to get around for the taskbar clause.
I totally agree with ThunderCat, but hypothetically if this game were more saturated, leave the full game runs as is but separate the Misc categories. Advantages and disadvantages are WAY more apparent in shorter categories but they make up for each other over time in the full game categories. I've used both, but prefer official releases for speedrunning, but emulators can have lag and some minigames are harder with mouse, whereas DS has no lag and minigames are easier due to proper input method. As well for vice versa. Though I read more comments above so maybe there's a lot more I don't know comparing the two platforms.
It all depends on what emulator and hardware you're using. If you're using MelonDS, I suggest DraStic as MelonDS is very focused on emulation accuracy, which is resource heavy, but I've tried both emulators and they run the EXACT same, so you're not at risk of emulation inaccuracies if you switch. Also try hardware acceleration if possible, like instead of using a software render for graphics, use OpenGL. Honestly, just getting a DS/3DS with the game is the best way to go since it eliminates all those issues. There's nothing wrong with pointing a webcam at your DS lol