Agreed. This is why I asked for sources.
I've searched pretty hard and have found no confirmation of a "fudge factor" or any other claims of inaccuracy in the PW calculation, intentional or otherwise, in the calculations.
In my experience, Megasquirt algorithms perform "as advertised." That is, they produce results in accordance with their documentation. There are no hidden "fudge factors" to protect users from their naivety or inexperience. An overly rich condition can damage an engine just as an overly lean.
I think I see the disconnect. The PW generator example you give is calculating PWs for running engine conditions. Megasquirt uses the ideal gas law to do that. (The spreadsheet you show may use the ideal gas law as well, but the formulas are hidden and password protected, so I can't easily tell.)
The TunerStudio Req_Fuel generator calculates the PW (time) required to deliver a quantity of fuel to produce a stoichiometric mixture in one cylinder' volume of air at a standard atmospheric condition (1000kPa @ ~70degF IIRC). This number is then adjusted by the megasquirt algorithm based on the amount of air the tune tells it is going into the engine (expressed as VE, or the percentage of a perfectly filled cylinder under standard conditions - looked up from the VE table) and the ideal gas law which adjusts for temperature and pressure. Again, no fudge factors, just science.
I might agree with you somewhat on a MS1, but this thread is about MS3, which while relatively inexpensive, is quite capable.