Goodbye warranty then. Many manufacturers have already been doing that with chip tuning, which is also just a software modification. When you take your car in for service they read out the ECU to detect chip tuning, and your VIN gets flagged in their system if it has been modified. So if at some point in the future you make a warranty claim, you are SOL.
Then there’s also the technical barriers they’re putting up, locking them down so unauthorized software can’t be flashed to them (much like Apple’s iphone and ipad crap).