Style described in App.xaml is not applied to Window in Fluent System.

### Description

We are testing FluentSystem, which was introduced in .NET 9.

The behavior is different when ThemeMoThde is described or not.

[FluentWPF.zip](https://github.com/user-attachments/files/20297477/FluentWPF.zip)

> When ThemeMoThde is not described

The Style described in App.xmal is applied to MainWindow and OverlayWindow.


> When ThemeMoThde is specified for System

The Style described in App.xmal is applied to MainWindow only.
The Style is not applied to OverlayWindow.
The Style of FluentSystem is applied to OverlayWindow.


### Reproduction Steps

Run [FluentWPF.zip](https://github.com/user-attachments/files/20297477/FluentWPF.zip), rewrite ThemeMode="System" in App.xaml and execute to confirm.

### Expected behavior

The yellow BackGround described in App.xmal seems to be the correct one

### Actual behavior

OverlayWindow described with Style that FluentSystem's Style is prioritized and adapted is adopted

### Regression?

_No response_

### Known Workarounds

_No response_

### Impact

_No response_

### Configuration

_No response_

### Other information

_No response_