In the NixOS community, the idea of "reset all system state on boot" is called "impermanence".
For websites the cookies tend to expire once every few months so I'll boot back to upgrade mode and refresh my log-ins everywhere at once every few months at the same time as I install my system updates.
You can also selectively copy some software's local data to your persistent read-write disk partition and create a symbolic link in the original directory, that way this particular piece of software will be white-listed in a sense and always writable. But I haven't needed to do that.
My only issue has been google which has a weird cookie implementation, it throws cookie-mismatch errors all the time so I have to delete them and relog-in every day. If it was a big issue I'd make my firefox profile always writable as described above but I don't use google much.
Do you mean you'd have a read-only base system, and a remote layer on top so the application data is only persisted remotely?
For my own files I have a partition which I use exclusively for data. When I want to make changes to the system I have a boot option to disable overlayfs which I use once every few months for updates.