Copilot in PF3 is off by my default settings. I made sure of that at least once by circling through all modes with ctrl+V until I got message stating so in the captions window. Also, in MCE, option to "answer to ATC if busy " is off.
The problem is specific to this AC only. In all others FO behaves properly and stays away from autopilot when he is not in charge of ATC.
When in MD11 PMDG, FO inserts ALT, HDG and SPD as per ATC instructions (PF3) regardless who handles ATC thus turning the pilot flying into spectator.
[ATC]
FoAlwaysDialsAfs=0 // will prevent FO dial in HDG, SPD and ALT at least when airborne
FoAlwaysDialsVHF=0 // will prevent FO to dial in VHF freq
These do not have any influence on FO at least in the MD11 PMDG.