No double standard here, the 2008 M1 was one of the best handling M1 ever, thanks to Rossi for the reasons Yamaha stated very clearly, what changed in the chassis geometry came when Rossi left, in 2011 and as a matter of fact (AGAIN) Zeelenberg was already there.
Then is that a double standard for Bradley Smith to do fast chronos on a full-specs 2013 bike while saying he can take more corner speed?
It's when the end of season shows the results that the difference comes to light and as you pointed out yourself, Rossi broke a leg in 2010, he didn't seat out only ONE GP like Lorenzo this year but 4, and still manage to finish 3rd with two wins vs Lorenzo's 9, since there was nobody else there to hold a real challenge to the Yamaha.
So no one can deny that both pilots and team managers have a direct influence on the development of the bike and the 2011 was already designed in view of Lorenzo being their first pilot, when they increased the swing arm length just before Le Mans.
This gives you the wheelbase he needs to carry as much corner speed as he did ever since but you can't have a bike doing this and being good on the brakes, enter corner as well and acceleratiing in a controled fashion as the Hondas does, as they kept complaining about all year.
Anyone who tried to drive both kind of bikes or learned about M-C mechanique knows this.