Congratulations on your new pup.
I think it is good that you want to acclimate her right away to being left alone, but the problem with your method is that she can still smell you. Dogs have keen sense of smell.
I also agree with LdyRev that with such a small pup, I would be concerned about leaving her alone for too long for fear of hypoglycemia. Breeders will often keep pups until they are at least 2 pounds for this reason.
With bathrooms, make sure that you have the lid of the toilet closed, and consider putting a child safety lock on it. There have been a couple of tragedies here on YT involving toilets. Little Yorkies often have amazing jumping and climbing skills and can surprise you.