Reproduction steps:
1. Open the attached project ("case_1249088-LoadAllAssetsIssue.zip")
2. Open the repro scene ("SampleScene")
3. Set the Play Mode Script to use AssetDatabase
4. Enter Play Mode
5. Inspect that "hiddenSub" log in the console
6. Change the Play Mode Script to "Use Existing Build" and enter Play Mode again
7. Inspect that no "hiddenSub" log can be seen and the order is as shown in the inspector for the object rather than in the serialisedFile

Expected result: Hidden files are not loaded and loading order matches between different Play Mode Scripts
Actual result: Hidden files are loaded and the load order does not match

Reproducible with: 2018.4.23f1, 2019.4.0f1, 2020.1.0b11, 2020.2.0a13
Reproducible with package versions: 1.7.4, 1.9.2
Not reproducible with package versions: 1.1.5, 1.6.2