The Danger of the "Square Foot" Trap
In residential roofing, you can often get away with a blanket "price per square" because asphalt shingle roofs have relatively predictable labor and waste. In commercial TPO (Thermoplastic Polyolefin) roofing, quoting a flat per-square price is financial suicide.
A 10,000 square foot wide-open warehouse roof with two scuppers takes a fraction of the time to install compared to a 5,000 square foot restaurant roof littered with 15 HVAC units, exhaust fans, pipe penetrations, and a parapet wall. If you bid both at $800 a square, you will lose massive amounts of money on the restaurant.
To estimate commercial roofing accurately, you must separate the field (the flat wide open area) from the details (the penetrations, corners, and flashings).
Calculating Detail Labor
Every penetration on a flat roof requires hand-welding. A skilled commercial roofer can roll out and robotically weld a 100-foot seam of TPO in a few minutes. However, custom wrapping a single HVAC curb or a complex pipe penetration can take an hour of skilled labor.
When performing your takeoff, you must count every single penetration. The industry standard is to add a minimum of $100 to $150 in labor cost per penetration, regardless of the square footage of the roof. If there are 40 penetrations on the roof, that is $6,000 in raw labor cost that a "price per square" roofer will completely miss.
Tapered Insulation Systems
Flat roofs are never completely flat. They require a positive slope to drain water. If the existing roof deck does not have a slope, you must build one using a tapered EPS or Polyiso insulation system.
Tapered insulation is incredibly expensive and complex to design. You cannot estimate this by guessing. You must send the roof dimensions and drain locations to the insulation manufacturer (like Hunter Panels or Carlisle) to have them design a custom tapered cricket system. The cost of this insulation can often exceed the cost of the actual TPO membrane.