Bench spots aren't going to be occupied by awesome players. They're bench players for a reason.
They were awful off the bench with bats last year, in theory Thome should improve that. God knows whether that really happens or not. They got enough other guys that can play the field semi-effectively to use a spot on a big bat like Thome.
But it's not like he's in the AL where he'll be getting consistent PT as part of a DH platoon. He's a great talent at the plate, obviously, but he won't be at 100% efficacy if he's just pinch hitting, even if it is once a game. Sure, he'd probably give a fair amount of value back if he played first, but he'd also be contributing a lot more offensively if he were in the every day lineup.