He's not an arse in general, but he knows this is a real struggle, we've discussed it before. I think it's exactly because he knows that it makes me feel so conflicted about saying no. If he really didn't mind not working nights because it affects me and frankly affects our marriage, why not just reject them outright, without making me responsible. He knows I hate it and that I end up really struggling, but I know I'm probably being unreasonable there and should just say no myself. I find that quite hard to do.
Does he really know? I’m asking because even when we accept what you say, I think a lot of us who are NT have difficulty really understanding. If you tell him you struggle but when he asks you if you’re okay with him doing it again you say yes, perhaps he thinks the struggle isn’t as bad as it is? He takes the time to check in and you aren’t honest with him, so he probably thinks it’s not as bad as it is.
If he’s not an arse in general then I think being honest with him might be the best bet.
On your separately bit, if you aren’t prepared to tell him you don’t want him working nights - Have you tried setting yourself up a routine for when he works nights? Would that work? Then when it’s a nights day you can say to your self “ahh, the day goes like this….” And when it isn’t you can say “The day goes like this…” So you don’t have “Routine” and “Upset Routine”, you have “Routine A” and “Routine B”.
So think about it a bit, plan it out. May be write it down. Think about things like when he gets in and when you’d be comfortable using the shower. If it would help, maybe have some visual cues that remind you you’re on “he’s on nights” routine - whether that’s using a particular mug or putting a picture of him on your desk, or wearing something different. Make the routine suit your day well but be distinctly different so it doesn’t feel like you’re just trying to get on with things and make the best of it. Do your dinner in a different way (especially important since you won’t be eating with him so you want to make something that’s nice for one and doesn’t leave you feeling like it’s the same as normal except he’s missing).
Think of things you like to do where he would cramp your style - whether that’s going out with friends or a soak in the tub with a good book, or binge watch TV he doesn’t like - and save them up for when he’s on nights so you have something to look forward to as well.
Have a bedtime routine that will set you up well for sleeping. Maybe shower at night if doing it in the morning feels awkward. Exercise can help with sleep. Use whatever relaxation techniques work well for you. One thing I would try and keep the same if it isn’t too awkward is the hours you sleep as your body clock tends to do better with this.
Also it sounds like you miss connection when he works nights - maybe the two of you could agree to write a note to each other each day. Not something big that you end up stressing about, just a small “I’m missing you”, or a selfie texted to say good morning/evening that you can add the odd thing to if something happens that you want to share. Or, if he’s not too dead on his feet when he gets in, you could have breakfast together in the morning.