I tend to avoid doing the merchant alliance voyages as they require finding items and sailing to a specific outpost. I would have thought that they would have given you traps/crates to collect the animals or items in but unless they spawn at the outpost you have to deliver the items or animals to then you have to go and find those as well and all of this on a time limit!
Is there an easier way to do these voyages? Normally I just sell gunpowder barrels to get the reputation up but that does nothing for the commendations.