Yes, I also think this is a bug. I filed it upstream: Executable bits are not retained with FileChooser portal
I don’t have any experience with Qt, but if you know your way around their bugtracker, it might be useful to file a bug there for the FileChooser directory functionality issue. (this might actually be an issue with the Platform Theme itself, depending on what your snap is using)
At the moment, all files chosen using the portal are remounted, even if the snap has access to the file using regular interfaces. Fixing this is on the long list of things @jamesh wants to do.