For a given displacement NA will always be more compact, and turbo will always have the higher potential power. For a given power, it requires working out a whole system's math because with a turbo you have not just a lot of extra heat load, but your block and internals have to deal with higher cylinder pressures meaning more weight. When they were working it out for the Valkyrie, for the target power, twice as many cylinders and NA worked out lighter, and more compact overall.
Heat exchangers and their attendant ductwork filled with fluid take up space and have significant mass.
So, no rules: it depends on your aero philosophy, and your need for peak power. F1 has almost always favoured developing your engine for max power, which allows you to expand your weight and downforce budget. So even if you have a little extra frontal area, and a touch more mass, if you have more power you're probably still going to be at an advantage.
the four immutable forces: