Those rooms are a little annoying I agree, especially the room to the left. That one was originally a large maze (that was mainly designed to waste time), but it was kind of annoying so I simplified it. During my playtesting I wanted to remove the little U-bend, but I didn't have enough time to change it. I never had any problems with running into walls, but I can def see that being a problem if ur not the person who designed the levels lol. I also agree the machine should be closer. I also wanted to move it closer, but I thought it might break the balance of the final challenge to reach the end, and didn't have enough time to test it, so I just left it as is.
As for the puzzles, I didn't pause the timer for the first one because I figured it's so close to the beginning room that it didn't really matter. And like you said, once you solve it once you're done, so any annoyance wouldn't really matter. I agree this was probably a mistake. As for it resetting itself, this actually makes the puzzles easier! They used to not reset, and if you made a wrong move or two, it was extremely difficult to recover from. I would get stuck for minutes trying to solve it. By making it so the puzzle always resets to a stable state, it ensures that you never get too far off track. Now.... obviously this does have side effects, like making it hard to understand what is even going on for the first puzzle, since you can't easily see the effects of stepping on a switch. And I wanted to change this! But also ran out of time. I also agree that adding a manual reset could have been helpful, but I thought maybe players would not use it properly. Like, the puzzle on the left is meant to be solved in two button presses, so it resets on the second press. The puzzle on the right is meant to be solved in 4 button presses, so that's how much you get. If I let players manually reset, they might reset too early or too late, y'know? Maybe this isn't actually a problem, I don't know!
The reason the timer is so low is because the whole main idea of the game is that you have to learn your way around the map in order to make it to the end in time. Each little nugget of information is supposed to make the game faster to traverse on the next iteration. If the timer is 5 minutes, the timer becomes basically meaningless. I might as well just remove the timer completely at that point! I do agree though that all the puzzles and the locked door rooms probably should have paused the timer. They did at one point, but I removed it because I kinda... didn't like pausing the timer? I thought it took away from the story of the game. I probably should have just left it though. I do agree the game can be extremely punishing if you keep running out of time and can't figure it out. I actually wanted to add an option where you can temporarily have infinite time just to test things out, but I didn't have time to add it! Again!
Anyways, thank you for your feedback! I may make a post jam patch where I fix some of the issues I and other have with the game. I'll probably implement pretty much everything you said lol (except for making the timer 5 minutes, I'll probably just add an option to increase the timer for a single loop or something)