nope the ending cutscene skip being on the first row is intentional
I don't know what to do about any of that and I gave up on trying to fix the scoring system a while ago haha
if you can't make it line up properly with what's on screen, consider making it just reward the player for doing anything at all, and setting the duration of each level manually. A couple times the sonnet finished and the game just left me on an empty screen where the score ticker counted down seemingly for no reason.