I think it's time to start trusting him more.
One thing though, since he hasn't yet learned how to signal you when he is out of the xpen that he needs to go, except with silent signals (Gus did this for a long time too), there is a good chance he will wait as long as he can...wondering why you aren't picking up the thoughts he has been desperately sending you telepathically 

 ...and then he'll just go.  
You might want to try bell training. It worked for Gus.