If I were to travel from Macau to Shanghai and to HK, would that qualify 72 hour transit visa?

Tom, the route is ok. However, you might still be refused to enter because the immigration officers might think you intentionally avoid applying entry permit. I have read some people who make use of this route like you were refused to enter when you arrive in Beijing.

To play it safe, I think you should fly from HK/Macau to another country and just transit in Shanghai.