for me they're a "last ditch effort". If I can't get something working correctly on NixOS then i'll just settle for the flatpak but it's not often that happens. for example I only have 3 flatpaks on my system one of which is discord simply because I found the voice comms work better with the flatpak than the native package.
I might end up switching to appimages though to see if they're any better.