I say, place it where it's most convenient. For stack height it really makes no difference. Your stack needs to be 2 times the length of the evaporator or 3' out of the roof or 2' above the highest point on the roof within 10'. Since the area is not over 20' wide you must be 2' above the top of the cupola no matter where it gets placed to meet national codes for solid fueled appliances (which a wood fired evaporator is).
Dave Klish, I recently ordered a 2x6 wood fired evaporator from A&A Sheet Metal which I will be converting to oil fired
Now have solar, 2x6 finish pan, 5 bank 7x7 filter press, large water jacketed bottler, and tankless water heater.
Recently bought another Gingerich RO, this one was a 125, but a second membrane was added thus is a 250, like I had.
After running a 2x3, a 2x6, 3x8 tapping from 79 taps up to 1320 all woodfired, now I'm going to a 2x6 oil fired and a 200-425 taps.