### 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(0, 2, GL_FLOAT, GL_FALSE, sizeof(float) * 2, nullptr);
		glEnableVertexAttribArray(0);
		glBindVertexArray(0);
		glBindBuffer(GL_ARRAY_BUFFER, 0); 
	}
	{
		
		glGenBuffers(1, &data.particle_quad_vertices);
		glBindBuffer(GL_ARRAY_BUFFER, data.particle_quad_vertices);
		{
			
			const float qv[16] = {
				-0.5, -0.5,
				0.0, 0.0,
				-0.5, 0.5,
				0.0, 1.0,
				0.5, 0.5,
				1.0, 1.0,
				0.5, -0.5,
				1.0, 0.0
			};
			glBufferData(GL_ARRAY_BUFFER, sizeof(float) * 16, qv, GL_STATIC_DRAW);
		}
		glBindBuffer(GL_ARRAY_BUFFER, 0); 
		glGenVertexArrays(1, &data.particle_quad_array);
		glBindVertexArray(data.particle_quad_array);
		glBindBuffer(GL_ARRAY_BUFFER, data.particle_quad_vertices);
		glEnableVertexAttribArray(RS::ARRAY_VERTEX);
		glVertexAttribPointer(RS::ARRAY_VERTEX, 2, GL_FLOAT, GL_FALSE, sizeof(float) * 4, nullptr);
		glEnableVertexAttribArray(RS::ARRAY_TEX_UV);