Automatic build profile generation disables `MainLoop` class

### Tested versions

Reproducible in: [4.3-dev-4](https://github.com/godotengine/godot/commit/df78c0636d79c9545a283e0e2a926d623998cc27), [4.2 branch](https://github.com/godotengine/godot/issues/2a8c429fcc19b042aaf43a51060c571d42ca2e39), [4.2.1-sable](https://github.com/godotengine/godot/tree/4.2.1-stable)

### System information

Godot v4.2.1.stable - Debian GNU/Linux testing (gcc12) - Wayland - GLES3 (Compatibility)

### Issue description

Automatic build profile generation disables `MainLoop` class without which I get an error which isn't printed into the terminal but is showed in new floating window:


It looks like `MainLoop` is one of the essential classes and engine can't work without it

### Steps to reproduce

1. Create a new project
2. Crete one scene (maybe not necessary)
3. `Project->Customize Engine Build Configuration...->Detect from Project`
4. `Save As`
5. Open the saved profile with editor and search for `MainLoop` inside `disabled_classes`

### Minimal reproduction project (MRP)

N/A

Reproduce the issue through Project → Customize Engine Build Configuration → Detect from Project, then inspect the saved profile's disabled_classes entry for MainLoop. Confirm the generated profile no longer disables MainLoop and that the resulting project runs without the reported error window.

Written by the indexing model from the issue text.