FWIW I figured out how to get a password manager (Browserpass, not KeePassXC) to communicate with flatpak Chrome if you want some advice on how to get it to work.
But yes, it was way more difficult than it should have been (which is “should work out of the box, just like a regular package”). So if you’re just listing some of the shortcomings of flatpak, never mind.
Keep an eye out, I’ll come back to this. It involves posting config file diffs and a script I wrote, it’ll be a longer post I don’t have the time to write right at this moment.
But yes, the fact that I need to find the time to post all the changes I needed to make to get this to work is part of the problem here.