Cat 1 minima is referenced to baro alt whilst Cat 3 is referenced to radalt. Therefore if you fly a practice autoland it is down to you which minima you set but you are still bound by the MDA. (obviously). Personally on a good weather day I would set DH, on a poor weather day, where I have planned an autoland in case of possible deterioration I will set MDA if the airfield has not declared low viz ops.
Despite the fact some people believe the autopilot will disconnect at
MDA -50, the aircraft will quite happily autoland.