Build it into the system
If the planes are so smart, it can't be too hard (well, alright, yes it can be hard - but not impossible) to update the software to identify the PF and crew on a flight, and choose a set number of minutes per flight for manual control at set events (course changes, approach, simulated technical issues, etc).
This all gets logged in the crew database and gets added as manual flying credits/sim hours of which there is a union/crew manager-agreed minimum per year.
As with movie nuke crews, the "this is a simulation" alert is played before any of those "issues", which will cancel if something real does happen. So, we don't get confusion over real events and the crews gain live experience which counts to metrics/targets - win/win.
Just my 2€ worth