Gifts sell well. Gifts are awesome. Gifts boost affection.
These are all great reasons for having a mission skill that returns gifts only. None of them explains why a mission skill that is supposed to deliver mats is useless for actually gathering mats.
The argument about scarcity is bull. None of this is planned scarcity, it's just a lousy UI that people have complained about since day one. It doesn't even do what you claim it does, because people can still game it to get five missions, by just relogging over and over or jumping on and off the ship. If BW does think they need to adjust mission yield for a system where you can start five missions easily, then they can adjust mission yield (and then nobody would be able to game it in any way to defeat this assumed yield control).
I have five companions. They are all at max affection. Like most crafters, when I log on to craft, I want to gather and craft, not jerk around logging and relogging fifteen times or hopping between zones trying to game a clunky, broken, slot machine UI into just giving me five gathering missions instead of five useless gift missions over and over. Make it do what it says on the tin: Gathering skills should allow you to gather mats, without hassle and without gaming the UI trying to just start the stupid missions.