Issue with saddle screws on a Player Strat

I’ve just picked up my second Player Series Strat in Buttercream. And I’ve noticed an issue with the saddle screws protruding which my other Player Strat doesn’t have (see last pic for comparison). The action is very high already so screwing then down isn’t really a solution.

I know they can be filed down but is the issue also with the neck relief? If they are screwed down can the neck be adjusted enough to compensate?

I’m leaving it in for a set up and I know it’ll be fixed but I’m just curious. And also curious how there is such a difference in how the saddles are set in what are supposed to be identical guitars.