One of the reasons people push for, say, firefox flatpak is because you don’t need to layer codecs anymore.
As another example, why people prefer the discord flatpak? because it is easier to push a update to flathub than to any disto repository, the rpm was outdated an unusable for a few days the last time there was an update, on flatpak it was updated in ~5 minutes. Now consider that you need people pushing updates to ALL repos from all distros vs just 1 single line of code change for flathub.
On the other hand tools like vscode, vim or emacs should be used in a toolbox. Yes, you have to layer hundred, if not thousands, of packages, but it is the only way that makes sense, and the only one that actually works for many specific usecases.
When I was figuring stuff out I even tried running gui apps in toolbox - it’s only viable if you use the default theme
You can install gnomes-themes-extras or something like that to use adwaita-dark for example, it will use the host’s config.