I don't quite understand the questions here. MAF reads airflow, not boost, so it doesn't matter what your airflow is.

Megasquirt determines fueling partially based on LOAD so whatever your MAP reading is gets inserted into fuel calculations. The one issue would be if you have multiply set to "off" because that prevents MS from adding fuel based on boost like it should so you end up having VE cells with 200% VE when thats obviously wack. I think load cells still top out at 255 so that is a bad path.

Last, if you don't care about your IC piping popping off then I wouldn't obsess about MAF accuracy since you don't seem phased by losing hundreds of horsepower. I would ignore MAF and spend that extra worry on building some braces that prevent your pipes from seperating.