Hm, I would sometimes tell her that I'm going to take a poop and let her know I don't really care if she knows I'm doing that- by that she could probably sense that you don't mind it that much when she does that.
Or you can simply tell her that she doesn't have to be embarassed about that. Being honest any open up yourself up first always works
. For example you can just tell her something (half-jokingly) like, 'you know what darling? Someone kids wrote that true love means you can brush your teeth while your g/bf is taking a poop in the bathroom behind you. And you know what? I think I trully love you.'
(When I told my gf that she was like 'EWwwwww' and then laughed her ass off.)
But I also think it's just a matter of time. After a while more trust and security is built between you two and you probably wouldn't mind anymore.