BMW's will only warrant claims on items that have not been modified, in your case the MAF is faulty which is part of the air intake system which has been modified. another example is if you fit an aftermarket performance exhaust they will not cover original cat converters fixed to the system. Some manufacturers wouldn't cover the MAF if you had aftermarket wheels because it has been modified.
Your best bet is to go to a different dealer with the original airbox put back in and they will then replace your MAF