We use a IO lift converted to DD. Fortunately this IO lift had very tall supports, and uses 4x4 wood bunks giving great clearance from prop to crossbeam. Our boat (SN196) can clear the crossbeam while under power, if the driver failed to slow the boat in time.
For bunk placement, the rear is as wide as possible to ensure that any side to side misalignment of the boat, the prop does not hit the bunks before the rub rail hits the rear post "guides". Note that we did not install additional guides, its only the lift frame posts that act as the guides if misaligned to the bunks.
The front bunks are narrower, and provide a bit of pinch resistance to the vee in the hull to stop the boat from going too far forward. Therefore, we have needed no additional stops or guides installed for the DD boat. When lowering the lift, we lower it to the point the rear of the boat is floating free and power off slightly. Same when returning, come in at docking speed and it settles into the pinched vee with very slight power on.
Been working like this for 6 years without any issue or mishaps.