I've almost never seen this. I guess that in the places I've lived, talking while using the loo is pretty much accepted as taboo. You just don't talk to people while they're doing bodily functions. It's like talking to someone while they're sneezing or having a coughing fit. You wait until their done. It's too distracting for a lot of people to follow the conversation otherwise. And anyway, some people have various downstairs issues which require a lot more attention than others. I'd hate to discover this by trying to talk to someone and be told that they need to focus on something fiddly, like replacing their colostomy bag or whatever. If you can't see someone or otherwise be sure if they're free to talk, either ask first, or just wait the 30 seconds until they're done. I feel this is the practical way to go.
DH assures me that it's the same in the gents'. Despite what they always show on television and in films, men apparently don't stand side by side at urinals, gleefully chatting away. At least, not in the countries where we've lived.
"MmmHmm" and other stonewall answers might be the only way to go, since I can see that if you just ignored someone (it's not like you aren't busy!), they might keep asking and get worse. Maybe a stiff, "I'm a bit busy here, we'll chat later," if they just won't stop.
In the case described by the OP, though, it sounds like she was trying to be polite, but didn't think it through. We hear noises all the time in bathrooms and are all pretty able to ignore them, and for all she knew, she was anonymous anyway until she spoke. And she disrupted the OP, who was not able to be seen by her and therefore could have been unable to talk anyway for all she knew. But I think she meant well. "MmmHmm. Okay." And nothing more.
Library Dragon, was the lady in your story talking on her phone while using the loo?
That's just ew
for the unknowing sap on the other end of the call. And is using phones in small public restrooms like using phones in lifts? Not sure. But still. Ew.