Eye strain might not be a good way to put it, it's more like something that screws with judgment when there are lots of bikes or I'm moving quickly on a boat. Shortening them away from 1:1 ratio or making them more transparent could work (bikes are thin so soft shadow is an intuitive justification to do that).
once they jump on a boat with continuous movement they’re no longer moving on a grid
Yeah, I noticed that boats screw with the offset before I noticed the shift mechanic. Grid movement in a puzzle game is usually a nightmare to do, but it's worth a try. Maybe you could manage fully unlocked movement too if falling into the water wasn't a thing.
As for failure states: The way I see it it's a game that I can take at short burst due to the difficulty and chaos, and picking the game up again is hard when there are all the same levels to replay while the randomness prevents me from being consistent. I mean that you could have some save points as in less levels but shorter day time (I'm not sure if there are currently any checkpoints further into the game). The pressure goes constantly up with the timer, difficulty and quickly learning new stages so a feel of relief could be refreshing. That's only a basic example though, and you could think of something more interesting.
...What if time of the day affected the levels?