Of course it would work, but would it work well? That's the question.
You have to take into account what bridge pickup you'll be using, so you get a smooth transition from one to the other. If you use a JB in the bridge and a squire standard strat single coil in the neck, it's gonna be wank let's be honest.
Do you change pickups mid-song or do you play a whole arrangement with one pickup? That's another question to ask yourself. My strat has lace sensors, if i'm playing a clean piece, i'll use the neck pickup only, but if i play something that has a distorted and clean section, i'll use the bridge because i don't like the neck pickup in that situation, some players will choose to flick the switch between transitions, so you'll want a smooth flow of sound without any huge step-ups.
What guitar is this anyway?