I don't know of (from experience) nor have I read of any lower alkalinity limit for brown trout. What is probable is that very low alkalinity streams in many areas of Pa receive such low pH rainfall that only brook trout populations, which as you know tolerate lower pH than browns, are able to survive. This particular Schuylkill Co stream has supported browns and some brooks for a long time. Although I have had pH concerns (lack of buffering capacity) for an equally long time, we have not had any fish kills or seen a reduction in the brown trout population. This suggests that pH does not reach critically low levels despite the poor buffering capacity of the stream.
As for other factors that determine whether a stream supports browns or brooks, field experience suggests that water temperature is the primary factor. I don't just mean maximum yearly temperatures; I also mean the number of days in a summer that fish are exposed to chronically stressful but not immediately lethal temperatures. The fish may tolerate the temperatures (barely) but their gametes may not.
I used to think sediment was more important than it now appears to be. I have found substantial (and surprising) brook trout reproduction in a few very silty streams. I am not challenging the idea that sedimentation/siltation is a problem for trout, but there may be some specific, limited, and very unusual circumstances where sediment, specifically silt, can be tolerated. What is maybe more important in this regard is not the appearance of the silt as it lies on the surface of the stream bottom, but how much it clogs the interstices and blocks upwellings in the areas where the brook trout spawn. How heavy or light the silt is per unit volume might also be a factor, which would be determined by its organic and mineral composition. As with most things in nature, it appears to be a more complex issue than what is often presented as being gospel. Having seen only two (Pine Ck, Schuylkill Co - trib to Schuylkill R; Hollow Run, Bucks Co., trib to Cooks Ck) such very silty situations in which brook trout populations were still thriving over a 36 year period of sampling wild trout streams across much of Pa. indicates to me how rare this must be, so the long taught general concerns about sedimentation in trout streams are still applicable with some rare exceptions.