We’ve heard from a lot of developers working on lower level system components that on package-based systems they can easily install niche command line tools for developers.

...However, after some discussions with the Flatpak developers, we have a plan for how to approach the distribution of third-party tools and we’ve already began prototyping. We’ll share more about this soon in a dedicated post.

I hope this system at least shares runtimes with Flatpak or else I will be severely disappointed. I'd be giddy if it's actually a case of flatpak offiically supporting CLI tools. It already does, and does it well, just missing a tiny bit of plumbing.