If you take a standard 4" square electrical box, one say 1-1/2" deep and another 2-1/2" and put them together flushed on the faces. Why are the knock out holes for each not aligned depth wise?
Seems most times you would want to mount them with the face flushed with the studs and if you did you can't connect these boxes to each other with a straight conduit because the holes are set at different depths.
I woudn't say those boxes (meaning "handy" box style) are most often installed flush with studs. More often I've seen them in places where the bottoms are aligned with each other, not the tops. Unless you mean a dougle gang box intended for switches and outlets, then yes I'd expect them to be face flush.