Is it legal for him to charge utilities on an estimated percentage of use? This is in Pennsylvania.

This would depend more on local housing codes. Such codes may require separate meters, especially for electric. But heating is generally done for the building. So its not uncommon for a bill to be prorated based on square footage and occupancy.

One of the commercial rentals I am using now, does the same thing. It is fairly common esp in rooming houses or houses that have been divided into two or three units.

Normally this is explained either verbally when you rent or in writing as to what share of the bills you pay.