The unmasking is in regards to Flynn at this point, and the best I can tell he was doing nothing wrong except he was not a person in the good graces of Obama and was going to work for Trump. Now remember this was during the admin transition, AFTER Trump was elected. This is when Biden was asking.
Once again, correct me if I'm wrong (Admittedly I haven't been following this super-closely yet), but since Biden was asking, Biden clearly didn't know who the subject in question was, correct, so how could he have been targeting Flynn specifically? If you were transitioning what is, literally, the most important job in the world in a period where you were concerned about what was going on, wouldn't you want to know everything you could to transition it properly.
Another possibly - in an ongoing investigation (which we both agree was legitimate), wouldn't you want to do everything you could up until the day you left to ensure that it was left in good hands? Yes, this plays into the "deep state is out to get Trump" narrative, but honestly - if there was a valid concern, the investigative agencies have a duty to the country to follow where it leads, do they not? Regardless of what you believe the Mueller Report, House, and Senate investigation eventually concluded, in January of 2017, there was still a lot of legitimate investigating to do regardless of who was in the Oval Office.