because "in" = general and "at" = specific place and I don't think the bathroom is specific or what?
You've edited your question so I will change my answer:
If you are in the bathroom, you are standing inside the bathroom, and there is a connotation that you are using the facilities.
If you are at the bathroom, it suggests it is your location but you are not using it, possibly on your way to somewhere else. You might not even be inside - you could be just outside, the point being that it simply marks your location.
In order to take care of your private businesses, you need to literally lock yourself inside the bathroom. When someone calls you while you are using a toilet or taking a shower, you don't usually say, "I am at the bathroom." You say, "I am in the bathroom."
According to Merriam-Webster, "At" is
used as a function word to indicate presence or occurrence in, on, or near
Especially when you are waiting in line to get in, you use "I am at (which means near) the bathroom".
People say I am staying at X hotel even though they sleep inside the hotel. People say I am at the party instead of in the party even though they will stay inside the place.
You cannot always say "at" is more specific than "in", or vice versa. In the bathroom is more specific in terms of meeting your needs than at the bathroom.
"He is at the table" means "He is eating at the table". In this case, at is very specific.
"In" is 3 dimensional; "at" is 2 dimensional. You would say "I'm at the bathroom" if the context made you think of the location of the bathroom on a plane or field or flat diagram, rather than in a building. Say you were tracing out locations on a blueprint, for instance. Or imagine that an explosion has blown apart a building, so that the rooms are now scattered over a wide area -- then if you were an investigator walking around the area, you could appropriately report that you were at the bathroom (if that's where you were).