It has nothing to do with that, your saying that the majority of the Enclave whom left Navarro to go on the couple of thousand mile trek did so in basic uniforms or combat armour; I find that a silly reason for them then aquiring the Brotherhood's Power Armour, if not just something implausable from any standpoint.
Ok then I will admit they had to have some suits of PA with them, but not enought to fight off the Midwestern BoS. What happened to those suits, I have no idea. I doubt they took all the suits Navarro had, after all some stayed at Navarro and they needed suits as well and Navarro was mostly civilians. They also had combat Armour at Navarro.
Anyways..
Midwestern Brotherhod under Barnaky end up Falling apart. A failed coup, sabotage, purges, decimation, desertion, settlement revolts and attacks against an enemy they helped create all combine to cause the downfall of the Midwestern Brotherhood. Decades fighting a losing war against the MLA and other factions, raiders, slavers and so on, cause them to fall back to strongholds across the Midwestern United States.
One Stronghold being the area around Chiago, the birth place of the Midwestern BoS (After they crashed there that is). They have been there for decades and should know every inch of it.
Enclave remnants from Navarro led by Augustus Sir, stop to make a relay station/out post. They are then surrounded by the Midwestern Brotherhood. BoS don't attack because they want the tech and they people behind it. They can't risk shooting them and killing them all. Even if they do capture any Enclave there is no guarantee those they take will help or even know about the Tech. Enclave out numbered can still do alot of damage. Midwestern BoS don't hate people and they are open to making deals and trading. They arn't knowledge hoarders.
Enclave under Augustus has to make the call. Fight these people or take their deal. Which is to leave some men behind to help make weapons and armour and other tech for the BoS so they can turn the tide against the MLA. Augustus was going to leave men behind anyways. Also they learn there is an army of mutants out there. Enclave need time to set up shop in DC and once again work on their plan to "take over the WORLD!" Helping these people stop this advancing mutant army will give the Enclave time. "Enemy of my enemy is my friend." Eden might as well be on the darkside of the Moon, he can't help Augustus in this Mexican Standoff.
The Deal is made and the Enclave move on to DC and the Midwestern BoS get some help. Once Enclave get but kicked again they have no where left to turn. No place to go to rebuld and try for a third time to take over the world. So the remnants become one with he Midwestern BoS.