Hello @nullproblemo
I found your post in a search because I am having exactly the same problem on Manjaro. Previously used the AppImage, everything was fine but the Flatpak wouldn’t find my vaults.
It is, I think, a problem with the Flatpak build permissions. The build doesn’t have access to your mount point, but there is a way to add it - but I came on here because I found that the change would automatically get reversed and I’d have to run the command again.
You can give the Cryptomator Flatpak complete access to your host file system, with the following command:
sudo flatpak override org.cryptomator.Cryptomator --filesystem=host
I preferred not to and manually stated where on the file system I wanted the Cryptomator Flatpak to have access to a specific moutn point, so yours would be:
sudo flatpak override org.cryptomator.Cryptomator --filesystem=/media/festplatte
You can provide multiple filesystem options, so you could do any number of mount points, for example:
sudo flatpak override org.cryptomator.Cryptomator --filesystem=/media/festplatte --filesystem=home
The above would give you access to the festplatte mount point and your home directory (including all subdirectories).
Hopefully one of the dev team might spot this and be able to comment/fix a later Flatpak build - I was searching for a thread to ask the dev team if they could fix it in a later build 
I love Cryptomator, recently purchased my supporter certificate. Brilliant piece of software. Hope this reply helps you 
EDIT: Should have said, best to run the commands without the Flatpak running - if it’s running you will need to restart Cryptomator for the changes to take effect.