And vice-versa I would imagine.

Having abandoned the Serco military, my Serco character Savet is now Itani Admired, and attempted to deliver CtC Xith, but was prevented from docking. Since the ability to work for the enemy is a legitimate game mechanic, the lack of ability to deliver war merchandise should be considered a bug.

It's a tarp!

It's a game-play mechanic of CtC, not a bug. You can not deliver cargo to the opposing nation.

I suggest then, that it is a bad mechanic. Why allow players to build enemy faction but prevent them from working for said nation in this one specific scenario?

It's not really intended for you to be able to build enemy faction when you're a serco/itani savet. I think you'll find this possibility will eventually disappear.