That's a very good question, or it could be both.
The Honda don't seems to have an issue and his very planted at the front, and i was thinking after the race that one of the issues of the 2013 factory M1 was slow/low heat build up causing the lack of front tyre grip during heavy braking, related to weight distribution and lack of set up options to correct that.
Yamaha addressed this with the 2014 chassis but Rossi uses the front a lot on it, and it is possible that he have to do that at the limit of what the front tyre can take, using the grip on abrasion more than on load with a difference between temperatures too high for the rubber to last (during straights the tyre cools down) and full lean, the tyre rubber degrades due to more extreme changes of temperature.
In short his chassis is better on the brakes for grip but not for durability of the tyre because it induces a high difference of heat between straights and full load, then tyre edge is overstressed by the abrasion due to high corner speed.
There is little consistency in the transitions imposed to the rubber due to the chassis geometry and the way Rossi is riding it, partly his style (brakes, gas) partly what is still imposed by the 2014 chassis (corner speed).
Yamaha still haven't find the "Rossi bike" balance I.M.H.O.