Reproduction steps:
1. Create a new 3D project
2. Open the Preferences window (Edit > Preferences)
3. Change any preferences
4. Close and re-open the project
5. Observe the Preferences window

Expected result: Preferences are saved
Actual result: Preferences do not get saved

Reproducible with: 6000.0.63f1, 6000.2.12f1, 6000.3.0f1, 6000.4.0a5, 6000.5.0a2

Reproducible on: Ubuntu 24.04
Not reproducible on: No other environments tested

Notes:
- Workaround: Create “~/.local/share/unity3d” directory
- Reproduction is not consistent
- A warning could be prompted up in the Editor notifying the user that the directory is missing