You can hack around the issue with projectiles by setting the ACU's hitbox to very small so that it paths around units a bit better, and then creating an entity attached to the commander with a hitbox. Then you can override the new entity's OnCollisionCheck, OnCollisionCheckWeapon, and OnDamage functions with the ACU's versions.
There is an example of creating an entity attached to a unit in the Aeon T2 Torpedo Launcher script. I don't have an example of an entity with a hitbox passing damage to the base unit, although I know it's possible since giving props projectile collision was an experiment we did.