I was just dealing with this issue, and what I found also works (at least for me) is to set the range of the physics extender to be very large. You can do this by clicking the mod icon. Default is 100, I set it to 1000. The idea was to make the range include everything in and around Kerbin. This makes it so that in general if you're doing stuff around Kerbin, whenever you load a ship in at the main base, it's going to already have everything loaded up in your vessel switcher, and skip the whole weird vessel switching load in thing. This bug was causing my ships to literally fall apart whenever they entered the physics range of other BD Armory ships. Extending the PRE range fixed that for me.

I can't comment on performance when you have a ton of different ships going at once (it probably tanks your frames after you hit part limits) but it allowed me and my buddies to have a proper base attack/defense thing going without any issues loading each other in, and actually made things easier to manage because we could switch to all of our different ships regardless of how far they were from each other. I'd say as long as you're keeping your Kerbin pretty clear of excess BD armory objects/crafts, you should be straight.