Well this aged nicely, I guess?

Interesting video! Something I never gave much thought to but definitely neat to think about.

One thing to note: I am very surprised you so quickly dismissed the Wario-Water Park connection. While it may seem improbable or strange, Water Park is definitely a Wario-themed course, at least to an extent.
Someone else already mentioned the big W logo as bearing Wario's mustache, but there is also an attraction called "Waluigi Sea bed" to the left of the starting area. You can see it if you pause the video at around 1:52.

As for Thwomp Ruins, all that comes to mind for me is Whomp's Domino Ruins from Super Mario Party.
Not sure if Sweet Sweet Canyon is outside of the Mario world, but it looks like some kind of joint effort between Peach and Daisy, based on the decorations/logos and such.
And if you're going to make connection to Super Mario Galaxy, maybe Cloudtop Cruise is set in Gusty Garden Galaxy? The theming and music seem to reference it heavily.

The possibility of Dragon Driftway taking place in the Chai Kingdom is actually really exciting. But speaking of Sarasaland, Shyguy falls could take place in the Easton Kingdom as the 2nd level and parts of the 3rd heavily feature waterfalls and caves within rocky locations, and based on the cover art of the game, would be the mountains. Plus, Daisy and shyguys have this sort of weird connection to each other

7:30 I know it's hardly noticeable, but Electrodrome isn't just one nightclub but rather an entire city. You can see numerous buildings surrounding you and there is also no ceiling, just a nightsky with the visible moon. It may be true that Electrodrome is a part of Neo Bowser City though

small correction but electrodrome actually takes place outside the club's exterior! you can tell because you can see the moon and buildings in certain parts of the map

My theory for Wild Woods was somewhere near the Somnom woods from Mario & Luigi Dream Team.
There's no definitive proof or anything, but I get the same general vibe from the two locations.

Super Bell Subway, N64 Ranbow Road, Toad Harbor, Mario Kart Stadium, and Toad Turnpike all take place in TOAD CITY,  this confirmed by the map seen in the subway.

A lot of locations are confirmed canonically and in-game by subway maps in different courses, and maps on monitor screens at Sunshine Airport.

For the F-Zero universe, FZ GP Legend actually reveals that Mute City is New York in the future. So that one is an AU of a real-life location! FZGPL also suggests Big Blue is its own one of several planets that appeared at some point near Earth.

The W does have a mustache though...

I think Thwomp ruins looks a lot like the board Whomp’s domino ruins from super Mario party and could be in the same area.

You predicted Mario kart World

Thwomp Ruins probably takes place in a Donkey Kong Location, since it kinds has a Donkey Kong vibe. And it would make sense.

these courses really seem like the rivalries are just for show and mario and bowser are just really chummy with eachother

Sunshine airport isn't exactly on Isle Delfino, but instead is the airport that took Mario, Peach, Toadsworth and some Toads to it. Also, the Koopa Beach in the background suggest it is nearby the N64 track (and maybe even the SNES Koopa Beaches)

3:52 counterpoint: The racetrack, anti-gravity and smaller size of the castle means this is most likely the replica of a famous in-universe location

Ah ye!!! I love Mario kart for this! I used to be much more active in a subreddit called "Marioverse" and there was a lotta discussion about this stuff!

Also, for Sunshine Airport, you can see the Rock from the old N64 Koopa... Beach? Koopa Circuit? So,  I always assume that it is on or around the Turtle shaped island we see to the east of Isle Delfino?

I think water park is in Wario city from Super sluggers since Nokis can be in both and the W is similar enough that they could be trying to use the Wario w but couldn’t get the rights

Now this is the type of world building I like to think about when it comes to the Mario Series. It makes these tracks feel more lived than just random locations floating in an aimless abyss

Who’s gonna tell em