Allik makes a big deal of worshiping Allomancers, giving them a different title every time, etc. I assumed this was a cultural thing since they don't have many Allomancers. But the others from his ship do not do this; the captain seems very short with Wax when they discuss the treaty. Is Allik just weird?
To explain the worship... Allomancers seem to be key to their civilization's survival.
Witness their magitek - a "primer" cube, that absorbs a type of Allomancy, which can then be used to power their flying ships. The only reason their expedition got as far as it did is because someone like Wax donated their power the first time. And, as you say, they don't have very many Allomancers to begin with.
Aside from that tech, other powers (like Feruchemy) are responsible for providing the medallions that allow them to survive at all. The southern civilization was freezing to death after the Catacendre, having adapted to survive during Rashek's time on a planet that was way too close to the sun, and living too far from Rashek's ashmounts that clouded the sky. Without the warming medallions to draw from, they can't survive. So it's natural for everything to revolve around those powers that allowed them to flourish.
This partially explains the worship, but not the varying reactions. Himarm's comment appears closest to the truth. Allik is an educated and cultured man - by his own description, it is required for him to meet a minimum standard to be on the ship at all. That's still a far cry from a Captain, who needs to know not only the culture, but the kind of culture shock that would go on with an accidental first contact situation like what they find themselves in. She can't worship Wax even if she was the same religion as Allik (which we can't presume, because he already explains there's several culture groups), because she knows he will not understand those values immediately, and that he's not one of the allomancers that has earned that worship or respect. When negotiating between nations, the need to represent her people from a position of strength outweighs any need to follow a particular ritual or dogma. Especially when (damnit Suit) they have proven they can be exceptionally hostile and inhuman.
Just to toss this last bit in there... Allik starts out urgently needing Wax's assistance, which colors how he treats him from then on. The rest do not (even if Wax was responsible for their freedom), and have the advantage of following their Captain's lead, as well.