Not supported means only "not supported" ->It may work .....
It does not mean you cannot configure this, and it does not mean limits are imposed.
It does mean that when you have any problems with this configuration, Cisco can refuse to accept a TAC cases for this issue.
and if they accept it , it will be only accept under least possible support conditions
To receive normal support you need to bring this to a supported configuration first ( replace the virtual APICs by physical APICs)
The main reason I can think off is that the Virtual APICs will have less processing power than the physical APIC, so performance will be unpredictable when the physical appliance somehow loses connectivity.