So I hopped in a train and used ctrl+click to send the train on a bit of a long trip. While I was en route, I decided to get a little work done in the sandbox. When I exited the sandbox, I couldn't get out of the train. Ended up having to reload from an autosave. Is this an unsupported maneuver?

I've definitely taken short trips in a train, used the sandbox during that period, then came back later to successfully leave the train. I just checked again on a short trip, and it seems fine to me. I'm not sure what's going wrong here, but if you can reproduce it, then I can fix it.

I can't replicate it from scratch, but it is now a permanent condition in my current game.

A quick aside - I'm suspicious of the hover car mod, I've had problems with it before where if the car gets destroyed while you're in it then you may have problems getting into a vehicle. As far as can I recall, this hasn't happened in this game. It's possible though.

I was wrong before: first, travelling isn't necessary and second, it's a problem entering or exiting a vehicle. So whether I'm in a vehicle or not, if I go into the sandbox and then exit the sandbox I will not be able to enter or exit a vehicle.

I have tried it with a spidertron (from spidertron tiers mod), the tank, the car, the train. I cannot enter or exit any of them after being in the sandbox.

BUT -- the hover car works. In fact, if I am stuck outside of all of my vehicles, I can get into the hover car and then exit it, and I will have access to all of my vehicles until the next time I enter the sandbox.

Mods:
Base Mod, Elevated Rail, Quality, Space Age
Auto Deconstruct
Blueprint Sandboxes
Fill4me
Helfima's library
Helmod
Hover Car
I'd like cliff explosives on Nauvis please
Mining patch planner
Nearby ammo count
Resources scanner
Spidertron Tiers
Squeak through 2

I've also disabled all of the mods except for sandboxes (and the space age mods) and loaded the game, the problem persists.

Again, I can't recreate from scratch so maybe it's just my game for some reason.

It definitely sounds like a problem caused by the Hover Car mod. One of that mods features is that it "locks" you into and out of driving via permissions in order to do its work. It does not handle permissions nicely, though, so it ends up removing you from your original permissions after it's done.

This mod also uses permissions to prevent you from cheating. Hence the conflict, or seeming like it's related to this mod. This mod works correctly, though.

You can resolve your issue by manually fixing your permissions. You should also report this to the other mod.

I've already opened a thread there too, thanks!