Flatpak Browsers cannot access files at /var/home but at /home

[ponychicken]

Describe the bug
This is i guess a complex situation happening when Silverblue, Flatpak and xdg-desktop-portal come together. It prevents users from picking a file to upload.

To Reproduce
Please describe the steps needed to reproduce the bug:

1. Open Nautilus and add a folder (like Downloads) to the favourite sidebar
2. Open a flatpaked browser and navigate to a site where you can upload a file (eg. some mail app)
3. Try to upload a file by clicking the upload button in the browser
4. A gnome file picker will open
5. Select the favourite you previously
6. The file picker will navigate to /var/home/username/downloads
7. Pick a file

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Nothing happens. (Some errors in web browser console)

Expected behavior
The link between /home and /var/home should be handled transparently to the user.

Screenshots
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OS version:

Version: 41.20241111.0

Additional context
Add any other context about the problem here.