They don't account for revenue from outside the stores. Apple technically doesn't allow purchases to happen outside its stores, in practice that has always been a bit of a grey area, but in any case that revenue is not disclosed to Apple and therefore cannot affect the rankings in any way.

As for the calculations, Apple updates roughly every six hours and I think (the algorithms not being public for a good reason, I have no real proof), they take into account the total sum revenue during the last period, but also use the relative delta revenue as a factor, so even with slightly lower revenue a suddenly popular app can appear higher in the rankings.

They also seem to change the algorithms every once in a while, we've seen pretty drastic changes overnight a few times, eventually though the top apps always normalize around the usual suspects, so it's possible that they just do some sort of reset of historical data that also affect rankings.