This overlay issue is bigger than just radar. I was in a 169 recently and the factory educated pilots 'discovered' that transponder returns are only displayed on the MFD in RA mode. In TA mode which is much more common for that helicopter operation, no returns are displayed.
Their training included a reasonable slug of time in a Virtual Interactive Procedure Trainer which is supposed to get you used to the controls and displays at lower cost than the full sim. Seems like there ought to be a lot more canned scenarios to display the quirks of the system.
However the problem is that nobody seems to be able to forsee the quirks until there is an accident to point them out.