My guess is that it's just like all the other EMS's have had for years - one baro sensor for realtime atmospheric changes, and another for manifold pressure. Normally with a single MAP sensor, the system takes a pressure reading of atmospheric air immediately when it's powered on... and bases it's Gas Law calculations off of that initial reading. But... say you are in a street car and you drive in a single trip up mount Baldy, 5000' then your EMS might have issues (depending on how it calculates required fuel)... with a secondary, real time baro sensor making continuous samples, corrections can be made on he fly without resampling.
Usually, BS3 and similar systems assume you're running closed loop Exhaust Gas corrections to make up for this, but when running open loop mode, it's nice for that fancy EFI system to make the changes automatically without having to sample exhaust gases.
GM did a white paper on this years ago, there's more to it than just manifold pressure (some people ask why the second sensor is necessary if you have manifold absolute pressure data realtime); the change in exhaust backpressure with significant density altitude changes throws a speed density tune off, by a lot.
BS3 is one of the most poorly documented systems out there, IMO. There are numerous hardware versions of it floating around and it's hard to tell what you are getting.
