Actually it does make a difference - to the ability to do the calcs at speed and constantly update them every second new data is added, which is what the PT CPU does vs. a once only calculation on a non-changing data set by software on a PC. Try doing the calcs on your abacus or with pen/paper every second that more new data is added.
Due to limitations of memory capacity and processing power/speed of the on board CPU, the firmware uses some processing shortcuts that introduce small rounding errors in the calculation of average power. It is usually no more than 1 or 2 watts at worst.
It is no more sinister than that. The downloaded data is correct and the average calculated from that data in the software is correct.