i don't know how many people feel the same way about people submitting runs from a video of another run, but i think its kind of a low blow to do one run and submit it several different times. personally i think each submission should be rerun of that specific run and not from a different run.
The thing is, a 48 Tracks run, for example, contains the same tracks and requires EXACTLY the same skill, luck, and inputs as a Retro Tracks run for that respective section. As it is, there’s essentially a 6-8 second penalty for submitting a section of a longer run if it isn’t at the start (plus the disadvantage of starting the first race without 5 coins), so if you’re really competitive about it then you should probably run it separately.
Another way of thinking about it—it’s similar to IL runs in other games, where there’s a leaderboard for segments of the game, regardless of what other parts of the game went well or not or even if it is run with other segments.
I don't see the issue with making one run cover multiple categories. There's an inherent timer disadvantage to this, as Pianist described, so if the player wants to optimize their times they'd still want to do each of the 69 categories individually at some point.
Not sure how other Mario Kart boards handle this, but as long as there's no timer advantage (for example, it'd would be really silly to be forced to play a specific cup via a 16 track run), including smaller categories from within the same run is perfectly fine here.