Thanks for playing!
The upgrade stations that were "rejecting" you are actually save points - the upgrade ones are supposed to be a special variant of the save points, I didn't consider that someone might take it the other way around! I probably need to give a clearer indication that the game is being saved when you interact with those, and maybe distinguish the ones that give you upgrades a little.
A tutorial for the central mechanic would be ideal, tutorial prompts in general were a last minute addition so I didn't end up having time to make something proper for teaching that.
That "skip" is the intended way up, if you're talking about what I think you are ;) I think it's cool that it feels a bit unintended though, I don't remember if I intended it to feel that way but I definitely noticed during development that it was a bit off to the side and felt like a hidden path, which I think works well as long as it's not so obscure it becomes difficult to find.