A quick comment about Sierra's BC firings; they do indeed use two chronographs, but only three screens. Both chronos are set up with S-1 as being the "start" screen, and the second and third screens (S-2 and S-3) being the "stop" screens for the two chronographs, resepctively. Bill McDonald and I have had many a long chat about this and this is his preferred method of doing it to eliminate errors caused by idiosyncracies of the individual chronos involved. I also used another setup involving two chronos with four screens, which was much faster and easier to set up. Bill eventually signed off on this route, but the BCs have been derived using both methods. I have no idea if they've changed anything in the past few years, but that's how it was done in the past.
The risks of using two seperate chronographs comes down to the errors inherent in complicating a system; more potential measuring errors, set-up errors, cycle errors in the units themselves, etc.. Best advice I can give here, is measure everything to the best degree possible, and then remeasure to verify it all over again. Distances need to be precise for the numbers to come out accurately (remember GIGO -"Garbage In, Garbage Out"). Also, make sure you know your atmospherics and apply the appropriate corrections. Hope this helps.