### Godot version

4.1.1-stable

### System information

Windows 10

### Issue description

When the project loads in editor, all the settings defined in project settings will be loaded over the default values, but when running the game nearly 95% of them will be ignored resulting in just loading the default settings.

here it's just loading only 4 variables from project setting and i have added the fifth in this pull request https://github.com/godotengine/godot/pull/80151
![image](https://github.com/godotengine/godot/assets/53877170/926168a6-e6d3-4983-b59d-7fd202db681d)

p_mat2x4[0] = p_transform.columns[0][0];
	p_mat2x4[1] = p_transform.columns[1][0];
	p_mat2x4[2] = 0;
	p_mat2x4[3] = p_transform.columns[2][0];
	p_mat2x4[4] = p_transform.columns[0][1];
	p_mat2x4[5] = p_transform.columns[1][1];
	p_mat2x4[6] = 0;
	p_mat2x4[7] = p_transform.columns[2][1];
}
void RasterizerCanvasGLES3::_update_transform_2d_to_mat2x3(const Transform2D &p_transform, float *p_mat2x3) {
	p_mat2x3[0] = p_transform.columns[0][0];
	p_mat2x3[1] = p_transform.columns[0][1];
	p_mat2x3[2] = p_transform.columns[1][0];
	p_mat2x3[3] = p_transform.columns[1][1];
	p_mat2x3[4] = p_transform.columns[2][0];
	p_mat2x3[5] = p_transform.columns[2][1];
}
void RasterizerCanvasGLES3::_update_transform_to_mat4(const Transform3D &p_transform, float *p_mat4) {