What a brilliant take on theme, I'm also really impressed with this being a GameMaker game!? I feel like that's almost a slanderous statement against GM and I'm just ignorant to it as an engine (which I think is probably true in this case!)
On the theme, I do really think it's well applied; but it's abstract in that it relies really on someone knowing what Samsara is and making a connection with time. So I potentially might say that with the power of hindsight you could have tried to be a little bit more on the nose with the theme? Perhaps a clock face spinning back in time, just spitballing. Really this is only to allay any accusations that the theme has been applied spuriously.
The application of time travel is excellent, and the bootstrapping mechanic works excellently. I don't play a great deal of puzzle games so it doesn't come too naturally to me, however I was able to bumble my way through. I totally understand you were up against it a little bit with regards to fleshing out the lore and getting it to work with rewinding, but there is enough there for the player to cut their teeth on.
I also thought I'd share one observation that I've had before which you might find interesting. I play a bunch of old-school grid based dungeon crawlers; and I have encountered games in the past whereby there is some sort of mechanic, timer or stat drain associated with the number of steps taken. For some reason this always makes me stressed and uncomfortable because it feels like a punishment for exploration. In this game that is not the case at all, but I still couldn't shake that feeling. It's a strange one, because I know it's all in my head, but I thought it would be interesting to share! And had minimal impact on my experience of the game.
This is a really nice entry, and I love the theme application and not just another wheel to spin. I had fun, thank you.