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I thank you for taking the time to respond and offering the best solution you could come up with, even if it isn't an ideal one. By pointing out the save game location you unintentionally lead me towards something resembling an actual solution, that I will briefly write here in case anyone else ends up in a similar predicament.

Rather than delete the save game listed under C:\Users\user\AppData\LocalLow\bubbles\Little Bug I moved it to the desktop and started the game back up, at which point it created a new save game (I made sure to get as far as the first checkpoint and then make sure that the hands were killing me; they did). It turns out you can open up the save file in wordpad and have it be almost entirely legible, so I started copying bits from the old endgame save into the new one to see if anything worked.

Eventually I figured out that changing the location to the final checkpoint (I believe it is named TheDesert) and copying over the X and Y coordinates successfully caused the new save to start at the last checkpoint, but it was still buggy. That said, I messed around and by increasing the X coordinate a bit (I think I upped it by 7) you spawned a few feet in front of the checkpoint and the hands once again killed you as intended.

The issue is that I still often come up short on those initial spring jumps and while I haven't fallen all the way through the floor at places I have gotten stuck in them for a bit so it is still not functioning ideally, but in this state it is likely completable. Personally speaking... this whole hullabaloo kinda burnt me out on the game if I am being honest (plus I was admittedly awful at it and would have struggled on that final run even without a week off), so I instead messed around with the X and Y coordinates in the save file until it spawned me right before the final jump, did that and declared the game beaten (ending doesn't run if you do this BTW which isn't entirely surprising).

Still I consider that closure and I walk away more satisfied than I would have otherwise, so thanks again for that last bit of info!

That's really interesting to know! I'm glad that you took the time to mess with the save data, that always yields interesting results. Something that crossed my mind: since your issue is based on colliders seemingly not responding to eachother, I wonder if turning down the graphics quality and screen resolution would help boost your frame rate and allow for better physics calculations. If your computers specs are not great, that might help. I'm sorry you didn't make it to the end, but I appreciate your foot work. Maybe one day I'll patch it when I have more time, but right now I'm deep in the next project. In any case your feedback has been really helpful, so thanks again and glad you played!