Well the transporter thing was because "he could do this", not because he was assigned to the transporter crew or sciences. I think he saw the problem as a "navigation" problem, which is why he came up with a solution the transporter crew did not.
That doesn't make any sense. That's like saying that a pastry chef could perform brain surgery better than a brain surgeon because she can bring fresh ideas. The only way he could've pulled off such a difficult feat of transporter operation is if he's an expert in transporter operation. And indeed Chekov's biographical profile on the official movie website states that he was top of his class in transporter theory as well as stellar cartography and is an expert in advanced theoretical physics.
The tactics used in the assult on the Narada might be navigational related too. Knowing where stuff is and what happens if you get near them sounds navagational to me.
But what you're doing is starting with your desired conclusion -- "Chekov is a navigator" -- and selectively interpreting the evidence to support it. That's backwards. The way to find the truth is to base your conclusions on the evidence.
This Chekov was born eight years after the timelines diverged, so his whole life history is separate from Chekov Prime's. He was even born four years earlier than Chekov Prime. So forget Chekov Prime. Forget your assumptions and expectations based on the old timeline. Treat this film as an entirely new, self-contained entity. Look at all the things the character named Pavel Chekov does in the film. Briefing the crew on a mission, performing a delicate transporter feat, engaging in scientific exposition and problem-solving. If you were totally new to
Star Trek, if you knew nothing whatsoever about Pavel Chekov (or the layout of the
Enterprise bridge) beyond what was shown in this film, it would never even occur to you that he was the navigator.
Besides, it's not like Chekov Prime was defined solely by his navigation duties. When he was first introduced, in "Catspaw" and then in "Friday's Child," he was a science officer, manning Spock's station while Spock was on-planet. We didn't see Chekov in the navigator's seat until "Who Mourns for Adonais?" After that, Chekov continued to double as an assistant science officer in numerous episodes and was often portrayed as Spock's protege. And he was often included on landing parties as well. In the movie era, he became the chief of security and then first officer of the
Reliant. So Chekov had many duties, as any command-track officer rising through the ranks would. He was never defined
exclusively as a navigator. And he was established as a science officer
before he became a navigator. So why can't he start out as a science officer in the Abramsverse too?