Yes. You can upgrade everything if you want.
Pickups would be easy. Trem block would need one specifically for Affinity thickness, but they make them.
Everything. You can replace/upgrade:
Tuners
String trees
Nut
Neck
Neck plate & screws
body
pickguard
wiring
pickups
saddles
bridge
tremolo block
potentiometers
switches
jack
Sometimes I change the strap buttons.... and also the knobs and tremolo arm...
I KNEW I'd forget something!Sometimes I change the strap buttons.
On a more serious note, I have pickguard templates for some of the older Squier Affinity series, and many of the other Affinity like the Jaguar Bass H, Jazzmasters, Teles, Basses. They're fun mod platforms.