The slower speeds in the long flat stages have nothing to do with doping or not. It is purely a matter of tactics. No teams wanted to take the front and up the pace, so it was slow. The same thing happens in amatuer races all the time. Slower speeds in the mountians and/or time trials could indicate less doping, but it will never be a meaningful indication since there are so many other factors (tactics, weather, stage difficulty and order, crashes, yada yada yada).