Hi
My deluxe strat has a different pick guard and pick up colour than the standard for the body colour. Gold pick guard and black picks ups on white pearl. This colour is usually on the black body option. I like the combination I've got.
Is having different combinations than the usual spec something they do on lots of strats and what would be the reason for doing this?

Since I change mine all the time, I can't give a good answer. I'm sure it's a listed option somewhere though, or, someone (dealer) special ordered it. I know a dealer around here that gets MIM's and Squier Standards and Affinity's and mods them with pickguards and pickup covers before they put them on the rack. maybe this is the case with yours. As a matter of fact, I think he even repaints a few because I don't remember neon green being offered as a standard Strat color MIM or squier.

i Like to change things up.

I ordered custom pickguards from ed roman and wd pickguard.

I recently replaced my ugly jim root telecaster white pickguard with a matte black pg to match the emg and flat matte body finish, the guitar looks killer.

My next pickguard may be for my strat or tele its going to be diamond plate either chrome or blacked out

Depends on the guitar's color but I prefer white pearloid.

I don't think mine was changed by the dealer I think it was done in production. I wonder if they have a few extra loaded pickguards available in a particular colour in production they just put them on. Having different pickguards though does really change the look and character.