If you have an unusual setup, it can be annoying trying to give programs permissions and sometimes it just outright doesn’t work. For example, I mainly game on a laptop which has a pretty small hard drive, so I tend to put most of my games on an external hard drive. Flatpak really doesn’t play well with that.
Are you using the dedicated GPU as your primary GPU or the integrated GPU? I’ve found using the dGPU as the primary can sometimes lead to suspend/resume issues.