Ball thrown into Dead ball territory

[MASS F/B UMP]

Federation Rules, R1 on 2B, R2 on 1B. Batter hits slow ground ball to F4, F4 dives and the drops ball. R2 slides into 2B and then F4 throws ball past F3 into dead ball territory.
Initial ruling R1 scores, R2 to 3B, BR to 2B.
Ruling after Offense Coach appeal to Base umpire - R1 & R2 score, BR to 2B. (Base umpire acknowledges that R2 had contact with 2B prior to throw by F4)
Ruling after defense coach appeal to both umpires - R1 scores, R2 to 3B, BR to 2B. Plate umpire states that runners get 2 bases from the base they were on at the time of the pitch. At this point Offense coach tries to protest game, Plate umpire states that this is not a call that can be protested, play ball.

I am a parent of player on offense, I also umpires fastpitch (ASA) and officiates FB (Mass HS - NCAA rules), I try my best to know the rules but this one makes me question my understanding of runner placement after a ball goes into dead ball territory. Is Federation different than ASA on dead ball runner placement.