Quote from GreezyBoys >>

"Once on each of your turns, you can cause the swarm to assist you in one of the following ways, immediately after you hit a creature with an attack:

• The attack’s target takes 1d6 piercing damage from the swarm."

The swarm is a magical swarm, it does not make an attack roll. If you hit a piercing resistant MOB with a non magical weapon that is piercing, you're personal damage is halved. The swarm does not do an attack roll, it simply reacts to your successful hit roll and does 1d6 damage. Clarification from WOTC might be good, but IMO the Gathered Swarm is not affected by resistances, because it is not doing an actual attack, just damage. 

 You may be right RAW. I'd probably house rule to make the swarm damage magical in my game though. 

I would hesitate to assume that no attack roll automatically equates to magical damage. It's probably much more about all the logistics behind that approach - an extra attack roll for just d6 damage bogs the game down quite a bit, you have to figure out what the attack bonus would be which could be different from the character's regular attack bonus, that kind of stuff.

That being said, in the same spirit of keeping the game moving smoothly I just treat it as an extension of the weapon. If the rest of the attack is magical, so is the d6. If not, it's not. This way you don't need to break down the damage into pieces when you're dealing with resistance. It's just not worth the time and trouble for what is ultimately a difference of 0-3 damage once a turn.