Thats because flatpaks treat each apps directory as their own $HOME so instead of $HOME/.mozilla its $HOME/.var/app/{app_name}/.mozilla
Which is still fantastic dont get me wrong. But Mozilla hasn't stopped hardcoding their Mozilla folder instead of the xdg dirs even throughf firefox issue tracker has had it on there for 20 years
Very very few companies I know of hire at that - except maybe in like New York and California where the cost of living is much higher anyways?