So i've noticed a thing with the modular armor while playing 0.7.1a (haven't updated yet, waiting for all the mods to complete the transition first):
Even if it's installed on allied, non-player ships it still default to being "player owned".
This means that if i call a general retreat my ships will escape but since the allied armor is tied to the ships they will never be able to leave the battlefield meaning that the battle will continue until the enemy ships or the armor is destroyed.
Let's just say this is somewhat annoying.
It is possible to make the allies modular armor to be NPC owned instead of player owned?