Flatpak is only for graphical apps - Flatpak's biggest flaw?

I love Flatpaks, the programs are nicely separated so they don't interfere with each other. They also don't have flaws like Snap's low performance or Nix's complexity.

But being limited to only graphical apps seems like a real drawback. If one wants to use Flatpaks as their primary package manager there have to be some awkward workarounds for cli programs.

E.g., the prime Flatpak experiene is supposed to be on immutable distros like Silverblue. But to install regular cli programs you are expected to spin up a distrobox (or toolbox) and install those programs there.

Having one arch distrobox where I get my cli programs from will not work, as the package entropy over time will get me the very dependency issues that Flatpak wants to solve.

So what is the solution here? Have multiple distroboxes and install packages in those in alternation and hope the boxes don't break? Use Nix alongside Flatpak? Use Snaps?