### 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)

glVertexAttribPointer(RS::ARRAY_TEX_UV, 2, GL_FLOAT, GL_FALSE, sizeof(float) * 4, CAST_INT_TO_UCHAR_PTR(8));
		glBindVertexArray(0);
		glBindBuffer(GL_ARRAY_BUFFER, 0); 
	}
	
	{
		
		glGenBuffers(1, &data.ninepatch_vertices);
		glBindBuffer(GL_ARRAY_BUFFER, data.ninepatch_vertices);
		glBufferData(GL_ARRAY_BUFFER, sizeof(float) * (16 + 16) * 2, nullptr, GL_DYNAMIC_DRAW);
		glBindBuffer(GL_ARRAY_BUFFER, 0);
		
		glGenBuffers(1, &data.ninepatch_elements);
		glBindBuffer(GL_ELEMENT_ARRAY_BUFFER, data.ninepatch_elements);
#define _EIDX(y, x) (y * 4 + x)
		uint8_t elems[3 * 2 * 9] = {
			
			_EIDX(0, 0), _EIDX(0, 1), _EIDX(1, 1),
			_EIDX(1, 1), _EIDX(1, 0), _EIDX(0, 0),
			_EIDX(0, 1), _EIDX(0, 2), _EIDX(1, 2),
			_EIDX(1, 2), _EIDX(1, 1), _EIDX(0, 1),
			_EIDX(0, 2), _EIDX(0, 3), _EIDX(1, 3),
			_EIDX(1, 3), _EIDX(1, 2), _EIDX(0, 2),
			
			_EIDX(1, 0), _EIDX(1, 1), _EIDX(2, 1),
			_EIDX(2, 1), _EIDX(2, 0), _EIDX(1, 0),
			
			
			
			_EIDX(1, 2), _EIDX(1, 3), _EIDX(2, 3),