### 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)

CanvasLight canvas_light;
	return canvas_light_owner.make_rid(canvas_light);
}
void RasterizerCanvasGLES3::light_set_texture(RID p_rid, RID p_texture) {
	GLES3::TextureStorage *texture_storage = GLES3::TextureStorage::get_singleton();
	CanvasLight *cl = canvas_light_owner.get_or_null(p_rid);
	ERR_FAIL_COND(!cl);
	if (cl->texture == p_texture) {
		return;
	}
	ERR_FAIL_COND(p_texture.is_valid() && !texture_storage->owns_texture(p_texture));
	if (cl->texture.is_valid()) {
		texture_storage->texture_remove_from_texture_atlas(cl->texture);
	}
	cl->texture = p_texture;
	if (cl->texture.is_valid()) {
		texture_storage->texture_add_to_texture_atlas(cl->texture);
	}
}
void RasterizerCanvasGLES3::light_set_use_shadow(RID p_rid, bool p_enable) {