my preference is off the shelf whether shooting carbon, aluminum or wood.
IMO if a bow is designed for an elevated rest, such as the Quinn and Hoyt GameMaster, then it's very acceptable EITHER way, but in the case of a 'custom' bow such as the Bob Lee or Wes Wallace bows, no...off the shelf. their sight windows and shelves are radiused and more often than NOT are cut to, or slightly, past center so an elevated rest would give too much "arrow left" (in the case of a right hand bow) making the bow more arrow spine sensitive.
the Quinn and the GameMaster are cut WAY past center to allow for cushion plunger (adjustable, elevated rests) installation.
the Martin Hunter, on the other hand, is designed for either...but it has a FLAT vertical sight window with a nearly flat shelf and is cut 1/8" past center so an elevated rest may be used if so desired.