Password managers are still too unreliable to auto-fill everywhere all the time, and manually having to copy paste something from the password manager happens regularly so it's not something that feels unusual if it doesn't auto-fill it for some reason.

I put the fault on companies for making their login processes so convoluted. If you take the time to do it, you can usually configure the password manager to work (we shouldn’t have to make the effort). But even if you do, then the company will at some point change something about their login processes and break it.

Indeed. I have to fill in my TOTP manually on Lichess and on tutanota.com. On proton.me sometimes. On other sites it always works, e.g. GitHub.