Flatpak "version" doesn't work properly ...

### What Happened?

1. Extracting a file to a location is NOT working on the real directory, but the flatpak "mounted" one. As the result, the files seem to be extracted, but don't show in "Files"
2. Trying to open (double click) a file in an archive shows "No applications found for ..." (works with "Files")
3. Show in files doesn't open "Files"

### Steps to Reproduce

**Extracting file(s)**
1. create a zip archive
2. In Files, open zip with double click (Archive Manager aka FileRoller shows up)
3. In Archive Manager use extract and select /tmp directory as the target
4. Use Files (from applications) to open /tmp directory
5. The extracted files are not listed in /tmp
6. Trying to repeat the process with Archive Manager shows the previosly extracted files already in /tmp.

**Open file in archive**
1. create a zip archive containing a json file
2. In Files, open zip with double click (Archive Manager aka FileRoller shows up)
3. In Archive Manager, double click json file
4. Dialog with "No applications found for ..." pops up, no applications are shown in the "select application" list except Archive Manager and Help

** Show in files***
1. create a zip archive
2. In Files, open zip with double click (Archive Manager aka FileRoller shows up)
3. In Archive Manager use extract and select /tmp directory as the target
4. "Show in files" doesn't open Files

### Expected Behavior

Restored functionality "before flatpak" (?).

1. Extracted files show up in "Files" in the "real" filesystem

2. Double click in Archive Manager opens a file for editing as it does in Files

3. "Show in files" open Files and shows the extracted files

### OS Version

6.x (Odin)

### Software Version

Latest release (I have run all updates)

### Log Output

_No response_

### Hardware Info

_No response_