No - the MAF will not be confused. If your turbo tries to suck more air into the system than the MAF can handle, then the ECU will just allow the system to run at the highest optimal level it can. You will never get the full benefit of the increased flow volume from a bigger turbo on a MAF equipped car.
Once you start to get over about 300kw atw the maf will probably be overun pretty badly.
If you can log it you can at least keep an eye on the hz you are seeing.