That is, perhaps, the biggest flaw with price per square foot as a metric. Not my favorite tool at all. Far too many things can render it useless when you're not comparing correctly. Apples to apples doesn't even cut it, you would really need to get down to Macintosh to Macintosh. Stick with broader metrics like size, price and location. If you want to get any deeper than that, consult a pro who does so regularly and has the experience to do it accurately.