### 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)

glBindBuffer(GL_ARRAY_BUFFER, new_buffers[0]);
		GLES3::Utilities::get_singleton()->buffer_allocate_data(GL_ARRAY_BUFFER, new_buffers[0], data.max_instance_buffer_size, nullptr, GL_STREAM_DRAW, "Batch UBO[0][0]");
		
		glBindBuffer(GL_UNIFORM_BUFFER, new_buffers[1]);
		GLES3::Utilities::get_singleton()->buffer_allocate_data(GL_UNIFORM_BUFFER, new_buffers[1], sizeof(LightUniform) * data.max_lights_per_render, nullptr, GL_STREAM_DRAW, "2D lights UBO[0]");
		
		glBindBuffer(GL_UNIFORM_BUFFER, new_buffers[2]);
		GLES3::Utilities::get_singleton()->buffer_allocate_data(GL_UNIFORM_BUFFER, new_buffers[2], sizeof(StateBuffer), nullptr, GL_STREAM_DRAW, "2D state UBO[0]");
		DataBuffer db;
		db.instance_buffers.push_back(new_buffers[0]);
		db.light_ubo = new_buffers[1];
		db.state_ubo = new_buffers[2];
		db.last_frame_used = 0;
		db.fence = glFenceSync(GL_SYNC_GPU_COMMANDS_COMPLETE, 0);
		state.canvas_instance_data_buffers[i] = db;
	}
	glBindBuffer(GL_ARRAY_BUFFER, 0);
	glBindBuffer(GL_UNIFORM_BUFFER, 0);
	state.instance_data_array = memnew_arr(InstanceData, data.max_instances_per_buffer);
	state.light_uniforms = memnew_arr(LightUniform, data.max_lights_per_render);
	{
		const uint32_t indices[6] = { 0, 2, 1, 3, 2, 0 };
		glGenVertexArrays(1, &data.indexed_quad_array);
		glBindVertexArray(data.indexed_quad_array);
		glBindBuffer(GL_ARRAY_BUFFER, data.canvas_quad_vertices);
		glGenBuffers(1, &data.indexed_quad_buffer);
		glBindBuffer(GL_ELEMENT_ARRAY_BUFFER, data.indexed_quad_buffer);
		glBufferData(GL_ELEMENT_ARRAY_BUFFER, sizeof(uint32_t) * 6, indices, GL_STATIC_DRAW);
		glBindVertexArray(0);