Rotators stop when they reach the desired location. Pistons have smoothing at the ends.

My flaps clip through the wing on retracting because the piston is smoothing out and the flap rotators reach the location too soon, and the flaps clip through the speedbrake (which is a few nudges above the flaps).

Edit: edensk came up with some code.

set the piston's speed to a very high amount (100-200%), and use the following code to adjust the actual speed:
smooth(Input,1/X)
Replace Input with whatever you have as the input, and X with the desired time it takes for the piston to extend/retract fully.