And for beginners, a flatpak is a particular way of bundling software so that:

A) all of the dependencies come with the program so you can just download one thing and run it

and

B) it has some level of sandboxing, which means you have some level of control over what the software you downloaded has access to on your machine. In theory.

So what they're saying is that if some software you want isn't already bundled as a flatpak, you're going to have a hard time with bazzite, as it's geared around making flatpaks easy, and requires more work to install things using other methods. Still works, just not as easy.