First, I've no experience with changing ECUs. The ECU interacts with other vehicle modules and you'd have to be sure that not only are the other modules compatible with that ECU, but that the signal ranges are compatible.
As for what the ECU is looking for precisely between those pressure sensors, I'd say that the closer they are to each other the happier the ECU will be. Some people have placed the two pressure sensors into a single small pipe (one into each end of the pipe) and that's apparently worked.
If they were really, really pedantic about it they could monitor variable fluctuation rates, depending on MAFS input, throttle position, engine load, boost pressure and coolant temperature - which would result in your 3rd option. I can't see them going to all that complexity just to determine whether or not the filter medium between the two sensors is blocked enough for a regeneration cycle. Then again, they did add (post 2010) an EGR sensor to make sure there's exhaust gas flowing through the EGR valve, so they CAN be pedantic if they want to!