We are not the maintainer for the flat pack distribution, we even didn't knew this exists.
Some time ago a user asked if he could distribute the flat pack and one of our devs said, that this is not a good idea, because of the file access rights (like you experienced)...
At this time i looked at this and it was not possible to add only read permission, or at least i did not find it...
On the other hand, whoever is building the flatpak could simply update the permissions to allow access to the host filesystem, depending on security requirements read-only to (almost) everything and write-access only to the home directory.
So you say, this is now possible?
It would be great to have some flatpack codeblocks... Will have to look into it....