Most likely ending to be cannon from my perspective is the "warrior destroys calculator ending" I imagine happening is that the brotherhood spend a long time elimating threats and uplifting the population, and educating them, spreading knowledge. Eventually they have there borders secure and don't really have a need or urged to expand, and instead study, maintain, modify, repurpose, the various tech they've collected. To explain them not being this giant active force that would rivial the Legion or NCR, they probably have a lot less active patrols, scouts, and contact outside of there sphere of influence, so the NCR could know about them from raiding Brotherhood bunkers before they were destroyed, but that's not likely seeing as how they've only recently expanded out of California and into the southern most tip of Nevada. The legion however, i believe Ceasar is aware of there existence, reason being that he is foucased destroying the NCR, (which would be a lesser power in this case) and expanding westward, gathering a large slave army. I remember from Lonesome Road Usslessy talking about a bunker that would have been of intress to the brotherhood of steel, and that Ceaser wanted it destroyed, being as how it had some considerable firepower in it. As for the Enclave, the way i see it they only destroy military assets when its a do or die situtation.
Example; From fallout 3 we all know that they could've, at any time, destroyed the Pentagon, Washington Outpost, GNR and crippled the Eastern BOS, but they didn't, but what they did do is destroy Liberty Prime, as it was assaulting their communications facility. They could've destroyed Liberty at project purity or any other time, but didn't. I'm make a wild jump and infer that this is because they lack the manpower, materials, and the time to build, or maintain any major assets due to their isolationist approach that is much like the Western brotherhood, minus the civilian brutality. Unlike either of these factions, including the Eastern brotherhood, the Mid Western Brotherhood protects the civilian, trains them,[ (more or less) for the record of course the inexperienced tribal recruits would have leather armor and some not so OP weapons, being as their not experienced , trained, or skilled, as opposed to seasoned warriors like the Warrior)(i confessed i horded the most advanced gear)]
The Midwestern BOS has The most valuable resource out of all the factions in the Universe; Trained people in abundance I'm not talking about the few hundred scribes knights, paladins, warriors, elders, and any other cast variation i'm talking about the various villages that, no matter what ending, get better education, irrigation, and basically become the brotherhood that's outside the bunker. With a large labor force, and the knowledge i'm pretty sure the Mid Western BOS could Convert it to motorized combat armor , repair some of the Vault 0 facilities, or painfully assemble the armor from scratch.(worth it though its totally bad ass in appearance)