Reproduction steps:
1. Create a new 3D project
2. Click Window > Search > New Window
3. Click on anywhere in the Main Unity Editor window

Expected result: Floating window stays on top of the Main Unity Editor window
Actual result: Floating window is hidden behind the Main Unity Editor window

Reproducible with: 2021.3.31f1, 2022.3.11f1, 2023.1.16f1, 2023.2.0b10, 2023.2.0b13, 2023.3.0a2, 2023.3.0a9
Not reproducible with: 2023.2.0b9
Couldn’t test with: 2023.3.0a1 (version is not available)

Reproducible on: Ubuntu 23.04
Not reproducible on: Windows

Note: This is also reproducible on macOS, but it was always like that there, so this is only a Linux regression