How Rare would it be to acquire a Gargantuan Squiggoth? Would this be modified if the Rogue Trader in question possessed the Peer (Orks) Talent?

With the peer talent granting a +10 to all fellowship test's with the appropriate group i would imagine it would if you throw in enough red paint and shineys... as well as some shootas so you can charm that green skin up and get him to drop the price. Hopefully without him taking your RT's hat!

Commerce is a Fellowship skill, AFAIR, so I'd guess you should get the bonus to that, which will augment your Acquisition roll. Here's hoping I'm not making crap up As for getting Peer, I'd make that kind of hard, as Orks are Orks, and puny Humies are puny, but Peer (race) is a thing, and if you can get it with the Eldar, who are much more arrogant, capricious, and known to look down on Humans as animals, or scum, and one can, you COULD get this, too. Personally, I've never been a real fan of such broad Peer talents, and would probably let players/ force players to get a more specific one, like Peer (Ork Klan), Peer (Ork type), or something, sort of like how you won't get Peer (Rogue Traders), but you can get Peer (Armengarde Dynasty). Some of the vaguer options of Peer/Good Reputation make me shake my head, knowing how little some organizations talk to their own parts, and how spotty communications further than "the moon up there" can be. Sort of like, if you have Peer (Orks), you would have a very broad talent, but if you had Peer (Klan Snakebites), you might actually get Enemy (Klan Goffs), as they don't like the weird, even by Ork standards, backwards Snakebites, or like how other Orks disapprove of the Blood Axes' stealthy practices. Of course, that's all up to you, and/or your GM.

Peer augments your Commerce or Barter skill, which permits a bonus to Acquisition. It's in the Acquisition rules, but essentially for every DoS in Commerce/Barter you act as if having +2 to your PF.