I just replaced the bridge and tuning mechs on a brand new Squier Affinity PJ bass just two weeks ago, so hopefully this info helps you.
The tuning mech holes were slightly bigger than 1/2". I know this because my 1/2" hipshot tuners fit in with some wiggle room. I used business cards to shim the difference and they now fit snugly and hold tuning very well.
I replaced the bridge with a Badass II and it fit perfectly, which I believe means that the stock bridge screw positions are to the typical Fender specification. I had a VM Squier a few years ago that could not properly accommodate the screw spacing on the BAII (I think the screws were closer together on the VM bridge but cant remember TBH; this bass had the "high mass vintage bridge", so it likely has to do with that bridge style).
As a comment to Squiers in general:
I bought the PJ Affinity two weeks ago with the intent of heavily modding the bass. Playing the thing fresh out of the box I was VERY impressed. I could never find a Squier of this build quality 10 years ago. The neck was set up very well (as far as my experience tells me); it was quick, frets were level, no jagged edges, awesome grain pattern on the headstock, and then some. Somehow, intonation was near perfect right out of the box. I'm convinced someone in QC gave this bass love. I wouldn't have a problem playing this stock Squier bass at a gig. As of now, the only stock items are the neck, body, and pickguard; everything else was upgraded.