What Flatpaks have you had dependency issues with? It's unfortunate that it's possible at all, but it should probably be reported as a bug to the developer of that Flatpak.
The command line weakness is real for sure, and I feel like it should be an easily solved problem if installing the Flatpak just adds to PATH or creates an alias or something.
This is why I think Kubuntu is a better suggestion than Ubuntu, and also Discover is better than the Ubuntu Software Center anyways and it makes it easy to avoid Snaps and does a good job managing Flatpaks.
You can also look at the bottom of the website where it focuses specifically on English users. It's 8.27% to 11.28%, still a big jump but nowhere near doubling.
I haven't tried Bazaar