How to reproduce:
1. Open the project "case_1245277-PackageVisibility"
2. Open the Package Manager window (Window->PackageManager)
3. Select the "Test Package" in the Package Manager
4. Click on the "Edit" button in the Inspector
4. Make sure that the Visibility in Editor would be set to Always Hidden in the Advanced settings in the Inspector
5. Toggle "Hidden packages visibility" in the Project window

Expected results: the "Test Package" and other packages are not shown in the Packages folder in the Project window
Actual results: only the "Test Package" is shown in the Packages folder in the Project window

Reproducible with: 2019.3.14f1. 2020.1.0b9, 2020.2.0a11

Could not test with: 2018.4.23f1 because "Toggle hidden packages visibility" toggle is not available

Notes:
1. It is reproducible when ""hideInEditor": true" is added to the Package manifest