Most boat lift manufacturers recommend to put the center of gravity of the boat in the middle of the lift. In some cases (mine) the bunks will end a couple feet before the transom. When a picture of a boat on a short trailer is posted there are many comments on "hooking" the hull. Will the same happen on a lift? Is there a good compromise on location?

This will absolutely happen on a lift, probably worse on a lift. Often, lifts have even less contact points with the hull than a trailer.

Such is the reason that Myco builds cradles for boat lifts as well as trailers. http://www.mycotrailers.com/MYCO-Custom-Boat-Lifts.htm

Not only do you need to have your bunks extend to or slightly past your transom, but they also need to be supported. 4 feet of wood bunks sticking aft of the last cross support on the lift is no better than having the boat hanging off the back of short bunks. A solution for this would be long boxed metal bunks that have a wood cap on them.

FWIW, also a boat lift must also be cut to fit/match step bottom boats. I have seen step bottom boats stored on flat bunks on lifts, and this can/will screw up the steps.