I really like the theming with the level evolving over time and seeing it change. That's very cool. There's a lot of games I've seen that involve somehow repeating the same level, and having it actually evolve on a geologic-ish time scale is one of the most effective ones I've seen, as it both means the level does actually change, but also makes a lot of sense aesthetically & narratively.
I think it is a very bad idea to send the player back to the beginning with a time limit. We are already replaying a similar level many times simply due to the nature of the level design--being forced to re-replay those similar levels again and again to win is very tedious. (Although, I'm not against tedium per se. But I don't know if that's what you were going for).
The music is also awesome.