Nah, it’s the same as with systemd, docker, immutable distros etc. Some people just don’t appreciate the added complexity for features they don’t need/use and prefer to opt out. Then the advocates come, take not using their favorite software as a personal insult and make up straw-men to ridicule and argue against. Then the less enlightened of those opting out will get defensive and let themselves get dragged into the argument. 90% that’s the way these flame wars get started and not the other way around.
For the record, I use flatpak on all my desktops, it’s great, and all of the other mentioned things in some capacity, but I get why someone might want to not use them. Let’s not make software choice a tribalism thing please. Love thy neighbor as thyself, unless they use Windows, in which case, kill the bastard. /s
That’s my main use for flatpaks too. Add to that any and all closed source software, because you can’t trust that without a sandbox around it.
Recently I’ve moved from using flatpak for electron apps and instead have a single flatpak ungoogled chromium instance I use for PWAs.