As long as one knows what modifications have been done and how to deal with them, there isn't any problems. Many diagnostic issues do not have textbook answers, that's for sure.
If a car is modded, you must think outside the box. If you like it inside the box, good for you!
I cannot see any connection with failed MAFs and mods. I have diagnosed failed MAFs on cars that have been chipped, not chipped, different air filters, etc., etc.
Either way, I'd just buy a 100 dollar Pierburg unit and be done with the whole damn mess. Period.
Just like aligning a car that has been lowered...you know the computer's specs are not going to be right, you have to formulate your own specs based on what the owner expects. The owner will understand that this takes extra work, and will pay for it. If they don't, they can go elsewhere.