The pulse stream looks the same either way. Further, if the mechanical assembly is moved when the computer is turned off then the position will be incorrect. Unless, of course, the computer recalibrates everything on power up. Fast Reads Most of the systems I've worked on required very fast response to each encoder pulse. Only rarely can one afford the luxury of polling a port to find that a pulse is asserted.
All polled loops are subject to varying degrees of latency.
This variable latency is sometimes deadly. Again consider the case of a car's distributor. Variable latency will make the engine run rough, since the time of each spark plug ignition will dither. In a high speed encoder system minimizing latency becomes a sort of search for the holy Grail. I've spent weeks yanking just a few microseconds out of the code to control the dither.