Hey hey :) Ok I see you've been messing around a bunch ^-^ and it actually fills me with joy someone is using the engine to make something!
I will try to go through the things in order as I understand them:
Global variable: you can put the variable on the window like "window.something = 2;". But putting in on a persistent object is also not a bad idea.
I never realized goToRoom is not in the reference, I think I simply forgot. You use it like this: "goToRoom(room0)", room0 being the name of the room (trash engine creates a global variable for every room/sprite/etc pointing to an internal room id). For trashovania I do some funny hacking to make the rooms work, I think, something like window["room_"+x+"_"+y], to access those global variables.
On findClosest: Calling this function on creation might not work, since the instances are created in a certain order, so it might not exist yet. Also for findClosest you need to provide x,y coordinates, if you just want to find any object use find(gamemode).
On the versions issue: Not at all sure what's going on. But relevant information is that trash engine stores game data in your browser. So if you make changes to, for example, trashovania, using the remix functionality, those changes will stay until you clear the indexeddb storage in your browser or use the "delete data" button in the settings. This is tied to the domain (like itch.io) and the game id (which you can change in the settings), so there can be some problems where different games access the same save data. If you go to the settings in your mod and change the id to something else that might fix it, but just a guess. The browser save data system was quite complicated to implement, and I'm not confident that there aren't any bugs in it. Also not exactly sure what kind of "upgrade()" you are referring to, kind of blanking on this one.
I don't think there really is a good way to use trash engine with version control. There is the save/load system, or you just export the game regularly and keep those as backups. The project on github is really just for developing the engine itself but the game is still stored in the browser (in the localhost domain).
I know this whole storage situation might be confusing it's not a very obvious system :d
Anyways, I hope I have answered your questions to your satisfaction! Unfortunately I am not developing trash engine very actively right now for lack-of-time reasons, but seeing the issues you run into gives me a good idea on which parts of the engine to improve when I get around to it! :>
(Also I'm on on my phone right now, but I will check out the mod, when I'm back on a computer)