Seemless shift gearboxes have zero effect on increasing engine reliability. Yamahas in particular has given it little acceleration benefit compared to Hondas, pretty much the only benefit the gearbox will have is the ability to have zero balance effect while shifting in corners.
Honda are simply better at making extremely powerful engines that are also reliable.
I heard from multiple sources (including Dave Emmett's motomatters site) that three of the four Yamahas (Cal, JL and Rossi) were already using their 5th out of 6th engines by Catalunya - 6 races into an 18 race season. This has meant there have been times where they have had to tune down the engines. In comparison, both Pedrosa and Stoner finished last year without even touching two of their engine allocation.
The biggest thing that could hinder Marquez winning the Championship is a big, big crash. His greatest strength right now is that he's riding without fear. That may change if we see him flung into orbit in an upcoming round.
it's actually probably gonna be a detriment to Yam's engines longevity. I was more talking about over a race distance as it will help preserve the tires which Rossi alluded to. He said over one lap it's not gonna make too much of a difference but over race distance, it will show.
edit: i base this on the last test they had with the seamless gearbox where Rossi was downshifting into a corner and the gearbox got stuck or something.