I'm thinking that the 2 damage is attached to the MM4 weapon that it's associated with. This is especially true in the case of Flame Blast (and Charge Kick since it shares the same association) which share the same damage as uncharged Pharaoh, it's associate weapon. Yamato Spear may have also suffered from this as it lost its shield piercing property that it had in vanilla MM6 and doesn't do it to anything in the game as of yet in this game (currently associated with Dive Missile, it may share some of its attack/damage properties).
The team probably needs to look over weapon data to see if there are some shared characteristics and re-purpose them again to make sure that the weapons from (at least) MM6 act like their original variants. Might need to look at MM5 weapons, just in case, for the same reason.
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I just tested all weapons on a Jumbig and found that associate weapons can still deal different amounts of damage. On the Jumbig, Toad does 4 while Gravity does 1 and Centaur does 2. Plant does 2 while Star and Skull do 1 each. Napalm can one-shot the Jumbig while Drill and Knight need two shots to take it down since that enemy is weak to Drill and its equivalents.
The associate system may explain the 2 damage regarding most of MM6's weapons, but the above example suggests that associates don't need to deal the same damage.
Also, Ring can pierce shields, but not Gyro or Tomahawk, which could mean associates don't really need to share the same properties either.