So we can agree that something targeted at "general user" should play nice with it, but making it a hrd requirement is too much for me

Flatpak is great for two groups of users: the ones who only use default settings in standalone apps and the privacy-oriented experts who know how to tweak things to their liking. In the middle is a large group of users who don't know or care how things work, but they want that one feature an app is supposed to do but mysteriously doesn't work with flatpak.

This password manager is supposed to work with my browser but it says it's not running.

App X says it needs app Y for feature Z, but I see both app icons installed on my desktop.

I found a guide online to enable feature D, but when I paste these arcane commands into the text box thingy, it just says ".config/AppQ no such file"

Even one of these occurrences is enough to make most users give up on that app or the OS entirely. I like the idea of sandboxing apps, and I use flatpak daily, but we have to acknowledge and hopefully improve some of its limitations or many users (yourself included, it seems) will consider it unusable.

My opinion on flatpak is that it only allows developers to be loosy with dependencies. I'm convinced it will fall appart in a decade or two because it's too messy and bloated as a technical solution.