Regardless of where the Brawly came from, if his opponent has beat him before last time, they have a better chance to beat him again.
And canon characters like this are really hard to play without giving them a headcanon that some people may not agree with, especially if you have to expand on a history that is kept hidden from us.
Also, he has a Hariyama in quite a few games. He has a Hariyama in the first, second, third, and fourth rematches in Emerald, and he has one in the Hoenn World Leaders and Fighting-Type Expert Tournaments in PWT in B2W2. If the two universes, one that has Mega Evolutions (with ORAS) and the other that doesn't (with Emerald and B2W2), are at least a little bit parallel without overlapping too much, I believe he would have evolved his Makuhita. Especially since we don't see him again after ORAS. So he would likely have a Hariyama sometime later, or already has one and just uses his Makuhita to fight people who are less experienced (like most gym leaders who have several different teams in different stages to go up against differently experienced trainers, which would honestly be smarter to do, as I think becoming a Gym Leader takes a bit longer than beating a Gym Leader and then taking over a spot right after the defeated Gym Leader, unless the process of becoming one was stated before in some medium we could use as reference).
