According to Zero, this looping is working as intended, if I recall correctly. So, these animations are almost unusable.
There is away to kind of limit the loop using wander options and raising the values more than that of idle animation, but yes Kirkfat we need ship animations with a once off value. (Like some of the ground emotes like WAVE.)
Although it be nice to be able to set the Durration below 5 the work around is to do this
Set the Wander weight at 5 and then set the idle weight at 4.8. Then use Warp in Federation Delay. Although this does work. But depending on the distance your ship is between the NPC Contact will have a effect on it to. So you may need to have them fly to specific location before the NPC warps-in.
Having your npc enter combat does seem to work. I have a mission where I have several klingon ships decloak right next to enemies. Once the combat is over, they don't seem to cloak over and over again.