They are only recently doing that as they don't seem to have the hirose connector at the factory anymore. So I think they may have stopped making AE-15/16 at the factory. In reality the pins are different too, but are the same basic shape and size that it works.
I normally don't file anything off on the heatsinks. I cut them with nipper pliers. I than dress the cut up with a file. I have actually used that ridge in the 5V as a backing against the 3V rectifier as a sort of locking device.
MTH uses many different heat sinks with only one side of the rectifier covered, so it is not an issue. G