The AC unit has a pan on the bottom, the drain allows water to exit the pan onto the roof. There is about 1/2 inch gap between the roof and the pan (the gasket thickness) That gap is what you don't want to seal. If you are doing liquid rubber on your roof, well worth your while to remove the AC unit, ( set on a piece of cardboard or plywood) paint around the opening, use new gaskets (not expensive) and put the AC back in place. OR paint right up to the edge of the AC base. The roof under the AC has not been exposed to the elements and should be in better shape than the rest of the roof.
Another discussion here:
A/C side view -"old-bisquit- posted this drawing that may help to see the layout.
