First, you're right about Rossi's and Stoner's struggles pertaining to the tires. It's been quite widely circulated that both believe the front tire is too hard and takes too long to get up to temperature. Second, Rossi doesn't prefer a hard front tire, he likes a really hard rear tire. IIRC he's ridden soft front hard rear most of his MotoGP career.
Imo, this new harder tire is actually conducive to a higher front end bias. If the tires are too hard at the front to get up to temperature, it means the bikes need more front end bias to raise the operating temperature. Rossi said as much in his interview with Italian TV according to the quote you've provided. Harder front tire benefits two people imo: 1. Lorenzo who rides a very aggressive cornerspeed style and who scrubs off a lot of speed with the front 2. Pedrosa who prefers a slightly higher forward weight bias b/c that's what Honda have always had (mass centralization is more front end than an L-twin Ducati).
Two people get burned by a hard front tire: 1. Rossi who developed the rearward-bias M1 2. Stoner who is accustomed to riding the Ducati GP which is naturally rearward biased b/c of the engine config. This season the "standard" Lorenzo Yamaha appears to be considerably better than Rossi's development. This is why Rossi said it would take time to win again. He was in the middle of developing the bike to work with different tires when he suffered the injury at Mugello.
Anytime Honda benefits by a change you're obliged to consider conspiracy, but the normalcy of the situation is so plain. If Bridgestone are going to use fewer compounds, they'd make harder tires to make sure the tires can always go the distance. Furthermore, if Bridgestone went out of their way to throw Honda a bone, Honda certainly screwed things up by building a new bike at the beginning of the season.
I agree it's the tires, but my technical interpretation is the opposite of what you have concluded. The tires like front end stress b/c it gets them up to temperature. Rearward bias is a disadvantage.