I have always used bigger TECs primarily to minimize the wiring. I have also sourced the TECs from one company (lazy) and at the same time and so these are quite uniform in thickness, specified and lapped flat.
I agree that before setting this base plate up, taggalucci should carefully measure them. I suspect that if they measure out then his bigger problem will be the plate. Unless your mill's spindle is dead on square then any surfacing tool ( and you must surface raw stock) will leave a very shallow scalloping at the center of the cut. Final flattening with a surface grinder is easy and better if available.
A interesting alternative would be to use the 0.5mm thick thermally conductive pads popular in the electronics/computer area. 3M makes these as well as others and they are inexpensive and available through over-clocker supply houses. This will also remove some concern in engineering the distribution of hold down screws to avoid bending of a flat plate as it is secured. A fair amount of pressure is required if using grease or indium and the all hard and flat conventional TEC mounting.