Is there anything that can be done to help the game as far as consistency in the puzzles? Currently they reset whenever the game is booted up (As far as I know), but it makes it a task to relearn all the puzzles before being able to do a run.

Would anything like a set seed or file manip be possible?

Hello, For my case i just don't save. If you save your game when you reset your seed gona be reset. If you clear the game without save your seed stay the same.

Yes exactly. Don't save your game.

If you're savvy enough you can make a save state though when you've got a good seed.

I can confirm this save behavior exists as well! DYA Games' other game Viviette has the same behavior with puzzle seeds. As long as you start your game from an empty slot and do not save over that specific slot, your seed will be preserved. You CAN safety save in other save slots (as long as you leave your original save slot empty), but I'm not entirely sure if it will affect the seed going forward (this is behavior that I still need to test, for both games too!).