I recently installed an audio analyzer called Spek from Flathub (via FlatDrake), but I found it would only recognize folders on the / partition where Flathub installed it. I made a post on the Flathub forum entry for Spek, and openned an issue one the GitHub page.
I was quickly responded to with the advice that Flatpaks often have permissions issues, and that I should try mounting the directory I wanted somewhere that Spek already had read permission. Of course, I had already tried that before opening the issue, and th directory was still invisible to Spek.
I resolved the issue by manually going into the Flatpak Permissions app that configures permissions for any SW installed from Flathub, added a new read-only permission with the path to the desired folder, and voila, the SW now works perfectly, and all done through the GUI. 
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I ran into the same issue in the past with other Flatpaks on Kubuntu and openSUSE, so it is definitely a Flatpak-related issue. But in the instances I was trying, it was Flatpaks being incapable of accessing SMB shared folders across the local network. Permission changes got it to the point where I could access one file at a time. But if I needed to do a batch of files, forget it. Much easier to just copy the entire batch to a local folder, work on them, and then send the updates back.
Flatpaks are not the perfect solution, despite claims made by the promoters on YouTube.
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