THe majority of my AA's do not include whole counties GRM, nor whole MSA's. The geography I serve makes this reasonable. I wouldn't take a blanket approach that it was necessary to take either a whole county or geography if the area makes sense. The ugly stuff is when you take half of AA #1, skip right over the middle (all low income tracts) and take the back half, even if you have branches on the sidelines of that middle area, THAT gets very questionable.
I have 10AA's by the way, none of which are contiguious and gosh darn it, I don't think I have one whole county in the mix but now you've made me so curious I have to check
I also do not have the entire MSA in either of the two in my state, just bits and pieces (which are contiguous but not the whole MSA).