There's a natural tendency to want to pick an easy to see aspect of the target: stack, cabin height, flight deck, but you probably wonder why the real guys liked to use the masthead height. By the way, their recognition manuals tended to give heights for stacks, masthead, cabin top and deck of most targets. Real sub skippers could pick whatever they wanted for their stadimeter range measurements.
But the accuracy of your distance calculation depends on three factors. The closer the target is, the more accurate your determination will be of course.

The more accurate your stadimeter angle measurement is the more accurate your distance will be.
But also the higher the measurement point is on the target, the more accurate your distance determination will be. Your error for a masthead height of 50' will be half that of a distance determination based on a stack height of 25' for instance. Your accuracy is directly proportional to the height of the aspect being measured. So whenever they could the real sub skippers used masthead heights, the tallest part of any target.
Stadimeters are nasty inaccurate enough without you handicapping yourself!