What Dave said with BMW's F series ECUs, they can only be bench flashed and that is a whole world of pain with regard to impromptu dealer visits, time taken to perform, losing maps with updates etc . Only they also know when tuning boxes have been plugged in, and log that too. JuiceBoxes claim to be able to wipe that record (although I imagine non-spec boost/fuel/etc levels will still be logged?)... but you're putting a lot of faith in trusting the JB has cleared it should you have to claim.
They've all cottoned on to how much they're spending in warranty claims to fix badly tuned cars. It only stands to reason they want to reduce that. It also means the introduction of manufacturer approved tuning, BMW already has its M-Performance line or Alpina. Mini their JCW stuff.... etc etc etc.