From all my experience with Fallout games, it may be story-mechanics dissonance, but .50 AP is definitely something power armor users do not want to be facetanking. The problem is that despite that, it hurts PA infantry far less than it would hurt a typical infantryman in lesser armor (as in terminally), in addition to such perks as helmet mounted sensors, incredible resistance to the biggest infantry killer on modern battlefields, explosive blast waves and fragmentation, and ability for one soldier to carry what is normally a crew served weapon plus its ammo and a sidearm or two. Short of advanced energy weapons and things normally used against light armored vehicles, good luck killing them, while each of them has the firepower of a heavy weapon team, the massive battlefield advantage would come out of the totality of such factors, rather than some kind of insane immunity to any weapons.
Now that advantage doesn't apply to fighting Astartes, who have the same, and are a product of thousands of years of warfare where this is the norm. Their standard guns are in fact light anti armor weapons, conveniently enough, as they often fight opponents with similar kinds of armor.
And that's i think is the big question. If the Brotherhood can figure out what are they dealing with and scrounge enough of suitable weapons to arm a big portion of their forces (plasma rifle, fat man, gauss rifle etc) they might have a fighting chance. If not, they will lose their numbers advantage before they start to adapt properly and lose badly.
It also depends on which chapter they would be fighting. Some of them are more specialized in guerilla and small unit combat than others, if it's something like Raven Guard or something like Space Wolves who are the "meant to be good at fighting other Astartes and equivalents" ones, they don't have good chances.
Also the Thunderhawk is going to be a huge pain for them to take down, they had enough issues with Enclave Vertibirds until they copied them and now everyone struggles to deal with theirs, but a Thunderhawk, this thing is on a whole another level, it's not proverbially a flying tank, it is in fact about as tough as 40k's tanks, and has even more firepower than those.