first of all, while I only had little time and thus a quick glance at beta 2, everything seems pretty impressive and well done. I like it.
now, for my point. from what I could tell, envoy ships have been turned into a totally peaceful/ economic unit. makes sense for diplomatic delegation. however, I think the allegiance sieging from beta 1 that the envoys had - while not perfect - was a pretty cool thing and I would be happy if it reappeared in some form. maybe another ship to do it, slightly altered, whatever.
I think I see the basic problem that you can't just make it a normal ship with this ability, otherwise it would be just as vulnerable as a siege ship and be blasted out of the sky. you have to make some protection, some way, how it works differently from siege. my thoughts go towards a ship that likewise has either stealth or diplomatic immunity or something that protects it from direct enemy fire. but it cannot be too strong to be overwhelming or too weak to make it useless. usual dilemma. maybe a lower level allows for expel, get them out temporarily, block the abilities. and then some higher one enables you to terminate the threat once and for all. at diplomatic cost?
in any case, it was something which I think has potential and I'd be sad to see it totally dropped.