It's not different. It appears to be a lack of understanding on the part of
the controller. There's nothing wrong with asking for a clearance to a
waypoint, I have no idea why the controller would ask for your destination
airport. If you had wanted an IFR clearance to an airport I'm sure you
would have asked for that.

Steve, Could it be a lost comm issue? Perhaps controllers don't want
to issue IFR clearances with clearance limits that are not airports?
I'm still not sure why it would be different for VFR-on-top though.
-Robert