How to reproduce:
1. Create new project file
2. Go to player settings in the editor,
3. Disable "Default is Full Screen" (this will hide the "Default is Native Resolution" option)
4. Do a PC Build and Run

Expected result: Either don't use the native resolution option when the full-screen option is disabled or, don't hide the option from the user
Actual result: Your default resolution settings will be ignored and instead you'll get a window that is the size of your native resolution

Reproduced with: 5.5.5f1, 5.6.4p3, 2017.1.2p3, 2017.2.0p2, 2017.3.0b10, 2018.1.0a5