It was said already, but I'll say it again: pay to play, folks. This conversation has been done to death amongst GTI owners, and there are always those who feel they can go against the explicit rules outlined in your warranty documentation and still have their car repaired by VW for free.
Flashing you ECU probably voids more parts than it doesn't- your entire drivetrain and just about any electrical part is probably not covered by Moss-Magnuson, due to the fact that they're all controlled by the ECU.
If your dealer wants to cover your repair under warranty after you have knowingly voided your warranty, consider it a gift. Just don't expect it.