Marner never really even played center in junior (beyond a few 10-12 game stints where his production plummeted), so I can't really see a move to that position at the NHL level being in his best interests as a player. He's got to stay on the wing, and he can still drive a line from that position.
Nylander, on the other hand, has been an elite center at both the SHL & AHL levels. He also had a 22-game stint as a center in the NHL at 19 years of age (playing almost exclusively with the likes of Colin Greening & Brooks Laich, who both washed out of the NHL afterwards), and he scored at a 20+ goal, just-shy-of-50-point pace, and was a positive possession player.
As much as it's fun having him and Matthews on a line together, I think he's still got to be the guy that you move to center in the long-term post-Bozak, and you could always replace him on Matthews' wing with Marner.