Intresting..wonder if its a political move since if it was included in the overall sales of the main chart certain games wouldn't necessarly have their number 1 posistion.
Possibly but there's no doubting it would be a massive change if they included digital data. Square Enix recently came out and said a third of their core games, not mobile or browser based, came from the digital space.
Considering that IIRC correctly, the top sellers charts are based on revenue earned(probably realtime updated as positions can change during a refresh). Yes. #1 seller on the world's largest DD platform? I'd call that a positive, even if for under an hour, for a game such as VC.
The changes are probably related to peak hours. Some hours have more people on, and some less. Obviously as more and more people get their hands on VC, it's position will change. A lot of people who didn't pre-order because of FFXIII, are probably buying their copies as we speak.
Also I do believe the peak performance for concurrent players yesterday on Steam was about 5,300 people. If I recall correctly, Alien: Isolation debuted with around 8,000 / 9,000 concurrent players for it's first day so that's another extremely positive sign.
Keep in mind as well that since this is revenue based and Valkyria Chronicles is a third of the price for Call of Duty: Advanced Warfare or Assassin's Creed: Unity, it means the game is outselling those titles in a 3 to 1, fantastic achievement for a 6 year old port. Now the interesting question is what does SEGA do next, port other core SEGA titles to the PC? Try to bring the whole Valkyria Chronicles series to PC (Slightly risky considering how much of a downgrade in cast the second one is.) or give the series one more chance but this time with a PC version to go with the console version(s).