Well, seems more or less your questions have been answered. I'm the one who buys the magazine and translate the charts. The best you can do is read the instructions i did in Neogaf. Point 3 is important, because maybe a game is selling 14k digital this month, but that's not enough since the game on the bottom of the chart is 15k retail + digital. So we miss its digital sales.
1. Tracked digital sales are from september 2013. There's no data available before that time.
2. November 2013 sales are missing. That means we have no data for games like God Eater 2, Lightning Returns or Project Mirai 2. Moreover, sales for other games, like Monster Hunter 4, are also missing on that month.
3. This digital sales come from a monthly retail and digital Top 30 Ranking. That means that if the game doesn't chart, there's no way to know its digital sales. So, a game can sell decently digital, but if it doesn't reach the 30 position in that ranking, there's no way to know how well or bad is selling digital. So, we should consider this numbers as the minimum digital sales, instead of a total sales.
4. This thread will be updated every month. Last update is June 2014 (new monthly updates games in bold)
5. The Famitsu digital sales are estimates based on surveys, and reseaches. The magazine says they use a website to do it, the poll is about 10.000 people for each system. They extrapolate and calculated the rest. It's the sample big enough to be considered accurate? Probably not, but it's the most official thing we have.
Point 5 is also important. Famitsu doesn't say how they do exactly get this digital sales, but on the bottom of the chart there's a note saying it's based on survays and research. I remember the first time they reported digital sales they were talking about how long they have been trying that system and finally they think they could get accurate enough to start these charts. I should try to find the issue again (not sure if i still have it). And translate exactly.
Since the Famitu sales come from Enterbrain and that's a famous and serious enterprise, i don't think they are just randoming numbers. I do think there's a quite margin of error, i also think that some games could be higher. But still i think is the most accurated thing we can find at the moment.
Media Create Annual Archive (Spanish version)
Essay Pro