TLDR at bottom.
On most linux forums, it seems that everyone is trash talking flatpaks, snaps, docker, and other containerized packages with the statement that they are "pre-compiled". Is there a real-world affect that this has with performance and/or security, and does this have to do with canonical and/or redhat leaving a bad taste in people's mouths due to previous scandals?
Also, it is easier for the developer to maintain only one version of the package for every user. All of the dependencies come with the package meaning that there aren't distro-specific problems and everything "just works" out of the box.
I understand that this also makes the flatpaks larger, but there is deduplication that shrinks them as you install more by re-using libraries. Do the drawbacks of a slightly larger initial disk usage really outweigh all of its advantages?
I have heard that flatpaks are slower than distro-specific compiled binaries but haven't seen a case where this affects performance in the real world.
TLDR: In most forums linux users tend to take the side of distro-specific packages without an explanation as to why.
I'll add my 2 cents to your very well written comment.
My biggest gripe with flatpaks notably, is the more difficult integration into the system. I use about a dozen flatpaks, and for every single one I had to tinker with flatseal to give them the correct access permissions, that I had to research online. One specific flatpak coulnd't even work with those additional permissions. Half of those flatlaks also will not follow my system theme and their GUI looks broken or out of place.
Given my limited usage of system themes to one that has flatpak packages (Materia) and tendency to go through the permissions of new flatpaks and tighten them anyway, those are good points to mention. For theming, it is definitely a trouble point depending on the platform and theme used. Especially when combining Qt5/Qt6 apps, Fltk, GTK2,3+, and GTK4 applications together, things may get even more messy than consistent theming on native applications. Having comprehensive theme packages for the theme you use almost completely resolves this problem. Though I doubt predefined customization isn't something that will be popular with some users given that ricing your Linux desktop to the extreme is a huge selling point of the Linux desktop for many.
I did forget about how especially with Flatpak and Snap how there is no actual guarantee that the default sandboxing permissions will actually be any good or even usable on many applications, which is an issue that partially comes from when community maintainers end up publishing packages for developers rather than developers or dedicated platform testers publish a given package (a common practice for many applications on the Flathub repository).
This always struck me as weird: the entire point of flatpak is to be isolated and not integrate into your system, why would you expect it to integrate with your theme?
I know they try anyway, but it just seems like a conceptual problem to me. They want to solve packaging by pretending it doesn't exist.