I am not a regular user of Zoom at all but I did install the flatpak to check it out. I am not impressed. A company as big as this and they couldn't scrape up the resources to find a developer to make a working client? PATHETIC!
It looks like it was done as a highschool project by the gifted nephew of the CEO for their computer class and then rolled out to the world so that all may benefit from the genius of the nephew.
I am definitely not a fan of Zoom either and had my own issues with the Linux client, but if the problems you describe are unique to the Flatpak and not in the official Linux distribution, you can't blame Zoom for that.