Transport Enemy Commanders

[zbehunin]

Is there any way that I might be able to modify the game so that I can transport the enemy commanders?

[Jools]

Modify which game? It's already possible in many of the games to transport (nap) enemy commanders, and it fact this is the default value:

bool transportByEnemy Default: true
Controls if a unit can be transported by an enemy transport. i.e. can it be kidnapped.