"Who is in the bathroom?"
I think there's no difference in the meaning, the same as "I'm in the bathroom" and "I'm inside the bathroom"! However, sometimes you do need to specify "inside" and duolingo is probably just trying to use a simple example to illustrate how to use 里 after a place-word, the same fashion as you use 上 or 下!
There are two sentences that keep vexing me:
In the first one we put location in front and use 有 as a verb, while in the second one we put the subject (well, question word) first and use 在. Is that a matter of topicalization? When the topic is location and focus is whats inside we use 有, and the second construction when subject is the topic? What about:
我的手机（在）洗手间里。- is 在 necessary? Is this sencence more like My phone (topic) is in the bathroom (focus).
洗手间里有一个手机。 - This one puts more emphasis on the phone? Like There is a phone (focus) in the bathroom (topic).
Thanks in advance!