Don't worry about the height difference in pistons.
When they will be in normal use, they just will never see the very bottom of the caliper bore, that's all.
Form me, i never gave a darn what can of paint that i bought at Lowes or the hardware store.
Krylon, or Rust-Oleum is as good as anything that your going to use.
Those calipers are never going to get that hot to bubble the paint off them.
