### 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)

int item_count = 0;
	bool backbuffer_cleared = false;
	bool time_used = false;
	bool material_screen_texture_cached = false;
	bool material_screen_texture_mipmaps_cached = false;
	Rect2 back_buffer_rect;
	bool backbuffer_copy = false;
	bool backbuffer_gen_mipmaps = false;
	bool update_skeletons = false;
	Item *ci = p_item_list;
	Item *canvas_group_owner = nullptr;
	bool skip_item = false;
	state.last_item_index = 0;
	while (ci) {
		if (ci->copy_back_buffer && canvas_group_owner == nullptr) {
			backbuffer_copy = true;
			if (ci->copy_back_buffer->full) {
				back_buffer_rect = Rect2();
			} else {
				back_buffer_rect = ci->copy_back_buffer->rect;
			}
		}
		
		RID material = ci->material_owner == nullptr ? ci->material : ci->material_owner->material;
		if (material.is_valid()) {
			GLES3::CanvasMaterialData *md = static_cast<GLES3::CanvasMaterialData *>(material_storage->material_get_data(material, RS::SHADER_CANVAS_ITEM));
			if (md && md->shader_data->valid) {
				if (md->shader_data->uses_screen_texture && canvas_group_owner == nullptr) {
					if (!material_screen_texture_cached) {
						backbuffer_copy = true;