Bigger injector's are no problem to buy, the eec just needs to know what size is there and a couple of other tables need adjusting e.g. the INJECTOR_OFFSET_TABLE which adjusts for varying battery voltage. The downside of bigger injectors is the emissions at idle.
Regarding problems with BOV, air reversal etc, a none recirculating BOV will cause problems as metered air is not going into the engine. I expect air reversal is catered for in the code. For example, there is a correction for fuel manifold wall wetting in the calculation of fuel pulsewidth and also a correction for the delay in manifold filling when the throttle is opened.
The idling calculation is very complicated and generally gives a better quality than speed density systems, maybe any idle problems are on modified cars where it's because the eec is so complicated something gets missed in the chip conversion.
But going back to my original query, I wonder how tuners are getting the results they are. Looking at Pro Flow's website again I see that for a flow 737. 17 kg/hr of air the estimated bhp is 233.3. As the standard MAF is shown in the code as topping out at 737.75 kg/hr in the MAF_TRANSFER_TABLE this would imply the eec wouldn't be able to accurately calculate the load. Either the MAF's are outputting voltages greater than 5 volts and the eec is still capable of reading this or the tuners are playing with the engine displacement value to lower the calculated load (pretty much guesswork without having a modified code to look at though).
More head scratching required!