Hey, thanks a lot for your in-depth comment on the game, I really enjoy reading thoughts especially about Intra-System since it was my first bigger game I helped to make. :D
I know it can be frustrating to search for the secret ending but I deliberately stopped speaking about secrets in games of mine after some information which I told in a private conversation were leaked. But I leak a small easter egg for you because you clearly put a lot of effort into it. If you click ten times or so on the big play button in the main menu there might be a message.
Regarding the meaning: I don't want to say if it is true or not but I really liked the interpretation of Joel Goodwin http://www.electrondance.com/the-lever/
I always disagreed with a skipping feature - I think the problem is mostly that the game isn't wide enough if that makes sense (more things like the broken lever, a few special events, more broad pathing and some other stuff), so that the repetition would be reduced or be a bit more spaced out - adding a skip-button would certainly be easier but I think there is a better (albeit harder) way to make it less tedious.
Thanks for playing! :)