The isolation paragraph seems more like a gripe with Gnome Software Center rather than flatpak itself.
It most likely doesn't scale to have all developers keep track of all the dependencies of all their software.
Also not sure I agree much with this. When developers don't keep track of their application's dependencies, end users often end up having to do it and it's a much worse experience overall.
I do agree with that it ends up being more of a burden on developers to maintain dependencies in their package. It's not great knowing there are potentially patched issues sitting in older libraries that are shipped with a flatpak because a package maintainer hasn't had the bandwidth to update them.
When I was packaging Flatpaks, the greatest downside is
No built in package manager
There is a repo with shared dependencies, but it is very few. So needs to package all the dependencies... So, I personally am not interested in packaging for flatpak other than in very rare occasions... Nix and Guix are definitely better solutions (except the isolation aspect, which is not a feature, you need to do it manually), and one can use at many distros; Nix even on MacOS!
Well; darwin users, just as linux users, should also work on making packages available to their platforms as Nix is still in its adoption phase. There are many already. IIRC I, who never use MacOS, made some effort into making 1 or 2 packages (likely more) to build on darwin.
I've been installing all my software on Ubuntu using the flatpaks because they are mostly up to date. They definitely have there downsides. I keep trying to save renders in blender and exports from draktable in my /tmp/ folder but it doesn't work right because of the isolation. Also running those programs from the command line or trying to run scrips included with darktable is a real pain in the butt.
One huge thing I don't understand about Flatpak is how, like the article says, everything is shoved into GitHub. Why? What is the rationale behind making each application its own repository just to store a couple modules and a YAML file?
I do like Flatpak though. It works for what I use it for, and it does a good job at keeping the applications I install through it separate from my system, so I can be sure that my package manager isn't going to brick everything with an update (not like that has ever happened though).