as far as I know it should be possible? was your home partition actually mounted at /home or another location?

I'm not completely clear on that based on your post.

What worked for me: I used to have multiple partitions, one for each system (Pop!Os and Manjaro, in your case) and one for the /home directory. The only stuff stored there is your personal data and settings. When you nuked your /home you must have destroyed something else.

Im not sure exactly how you borked it but you can generally just point the popos installer to your old home, it shouldnt format it unless its flagged for format during the install, make sure it isnt and you should be fine.

Home does contain config files that might mismatch depending on the version differences between manjaro and popos, but not sure if it will cause much problems

Mounting the home partition at /home in the installer should work. Deleting the /home of the user you're logged in as isn't going to work because the applications you use to do it will most likely try to write something into ~/.local or .config, do it's never really empty. You could log into the root user though and do it from there.

Btw. It's not really beneficial to put your home partition on an HDD for the same reason. All Programs you use are going to have to access some hidden config or data files so it's going to slow everything down. (Also in case you use Steam, it installs all the games in ~/.local) A better way is to mount the HDD somewhere else and symlink your ~/Documents, ~/Pictures etc to the HDD.

Should be "trivial", yes. The central OS components (e.g. systemd or whatever) shouldn't care about anything in your home directories. Only apps that store your user preferences, user DBs, etc. there should. So you might have some old hidden directories that won't be used anymore, some that hopefully different versions of the same apps if applicable can migrate the data from, etc. But it shouldn't affect the general functioning of your OS.

It wouldn't be a bad idea to first 1. backup the home directory, in case any app data migrations mess things up somehow, and 2. create a user (with sudo permissions) with a home directory path that didn't exist in the old dir structure, in case you need to login as that user to fix things (e.g. let's say your profile or shell resource script has something that a new shell version in the new distro doesn't understand and that keeps you from logging in).