Rear routed bodies have slightly thicker tops where the controls mount, as opposed to mounting them on a pickguard which is usually no more than .090" thick. So, sometimes some adjustments need to be made.
For blade switches, I don't recall having to do things, but I believe Schaller makes a switch that's not quite as deep. Still, screw spacing should be the same. You may want to call Warmoth and ask if the switch they sell is different from the typical Strat part.
For pots, you may need long shaft parts, as opposed to the standard. Note for future reference: always buy the long shaft pots. You can adjust them to fit in just about anything by putting jam nuts on to set the depth.
As for felt or something to protect the finish from rubbing knobs - no. Get the right pots. Otherwise, they'll just be too tight to rotate effectively.