Black screen when running the game without the embedding feature (not reproducible in blank project)

### Tested versions

- Happens on the latest stable version (4.5).
- Didn't happen on previous versions (since there were no embed support on MacOS)

### System information

Godot v4.5.stable - macOS Tahoe (26.0.0) - Multi-window, 1 monitor - OpenGL 3 (Compatibility) - Apple M3 - Apple M3 (8 threads) - 8.00 GiB memory

### Issue description

The new embed game feature presented on the latest release for Mac, my game runs perfectly fine, but when trying to run the game without this feature, on a default floating window, it's completely black.

### Steps to reproduce

When using a `SubViewportContainer`, the game window sometimes turns completely black when I don't use the embed game feature . This only happens in my main project, not in a new blank project.

https://github.com/user-attachments/assets/aed44cd2-185c-472b-97d7-281bdfbe16c6

On this project (my commercial one), I have a SubViewport container and the black-screen issue happens:

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On this basic project with just some Nodes works fine and no black-screen is found:

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Edit 1: Urgent, happens on the exported game too! 🚨

### Minimal reproduction project (MRP)

Can't provide since it's my commercial closed-source game, sorry. For some reason it doesn't happen on any other project like mentioned above.

No source files, tests, or code entry points are mentioned, and no minimal reproduction project is available. Start by reproducing the issue with SubViewportContainer in the reporter's project in both embedded and floating-window modes, including the exported game; done means identifying a reproducible cause and confirming the black screen is resolved without regressions.

Written by the indexing model from the issue text.