My first take on this is that it's a -laying back- issue with him. Maybe he arches his back and squirms when layed down for a nap because he doesn't like to be tipped back like that and then feel pressure on his back. And maybe he struggles when put in the carseat because that tips him back too. He also probably doesn't like the feeling of being immobilized either but, I suggest that issue is not the main one even though lots of babies don't like being strapped down.
Resistance to being tipped back is a sensory issue that is common and normal. Parents are usually pretty quick to figure out that baby calms down when being held upright to the shoulder, bounced, and walked around to calm down. Or that baby seems soothed with pressure on the tummy, which can be done by holding baby face down across your lap. It's soothing to them just lay across your lap as you sway your kneese back and forth slowly. If you do this, just cup baby's head in your hand so that the head isn't dangling there. Belly babies are also commonly belly sleepers as well. My kids were belly sleepers, but not on flat surfaces. They always needed a clump of blanket to curl their bodies around. I think they needed to feel the pressure on their tummies and something to hug onto. Kind of the way I sleep with my body pillow (which is not my husband, ha ha).
The reasons for seeking out or demanding belly pressure and face down position, rather than the head back position could be because of colic, acid reflux, sensory issues around being tipped back, and any number of things.
It sounds like he's doing a pretty good job at training you though...You are a smart and intuitive Momma to have figured out that he likes the upright positions better. I'd continue to follow his prompt and go with it.
A trick: My little one would get nausious in the car when his carseat was tipped back flat. I figured out that I could place the carseat upright as much as possible (allowing his head to remain comfortable), buckle the seat belt real tight across the front of the carseat to hold it in the position, and then, I'd wedge a small cushion pillow in the empty spot behind (under) the carseat to avoid slippage. This was in the days, when my son was still in the rear facing car seat type. So, my front/back might be messed up. I refer to the front as around the feet area where the buckle goes across and the back as in the back side of the carseat. Sometimes the wedged pillow would pop out of position, but it was easy to just poke right back in.
I came up with this after one terrible experience of him burping up a bunch of formula only to choke on it as it pooled in his mouth while I was driving and could not help immediately. It may have been a symtom of acid reflux, but I solved it without meds by adjusting him into a more upright position so that the spit ups would drip down and not get caught in his mouth. However, I do realize that the intensity of acid reflux varies and some kids do require meds, some even more such as surgery.
But, hey, these simple solutions worked for my little guy. He gave us the lead and we listened to him. Still to this day, my little non-head tipper prefers the water dumped over his head in the bathtub rather than leaning back for a shampoo rinsing. Not a problem.
God bless, Good day,
You're already doing a great job at figuring out what he's trying to tell you. Keep up the good work. What a wonderful Momma he has.
YM