I think there may be some change of value of the BER measurement done in these two ways. if we set PRBS generator to use layout bit rate then PRBS and pulse generator will provide same result as we get by using 3R regenerator. whereas if we set PRBS bit rate with some defined rate then result would vary from 3R regenator. I have noticed in many cases 3R regenartor calculates on the basis of layout sample rate. so we can differentiate the response ofthese two on basis of its analysing parameters such as bit rate.