I would use the pass-thru if I was using two amplifiers in different bandwidths or different zones. Just as Jim said, these are buffered outputs on the pass-thrus so there is no loss of voltage because they have their own output OP amp.
However, if using two identical amplifiers to drive symmetrical tower speakers or two identical subwoofers, then I would externally divide the RCAs and not use the pass-thrus. Because the pass-thru is buffered, the gain setting on my two amplifiers would be different. Nothing technically wrong with that other than it makes me uncomfortable.