I personally don’t think that creating a script is a bad solution. The entire Linux eco system is based around composable components (especially when we talk about terminal commands). Most of the Flatpak applications are available through GUI menus (.desktop files) and that’s the focus of Flatpak. And I think it’s a design decision not to expose every application as a separate program in the $PATH by default. This way there is less of a chance to collide with anything random on the system, if they have the same name.
Having said this, I still agree it would be beneficial for most users if there was a way to automatically create scripts in a special bin folder, that is available in the $PATH. The problem is, what application name should it have? What about different versions of the same program? The entire Flatpak concept was not designed for this, so creating a script for your personal use is not a bad solution.