If you were a clothier and started altering designer clothes and selling them how long do you think it would take till Jordache or whoever knocked on your door?
If you bought a designer suit and hired a tailor to hem the slacks for you, should Armani have a case to sue?
Once you pay for the item, it's yours to change any way you wish, IMO. As long as your hypothetical designer clothing alteration business didn't attempt to pass the clothes off as original, unaltered work, I see absolutely no problem with that at all.
These businesses clearly and openly altered the content of individual copies of movies. They didn't try to deceive customers into thinking they were selling the original work of the studios. Every copy sold came from a separate, legal copy.
In addition, these same studios regularly do the very same thing to their own movies in order to show them on network television. If the practice is so patently offensive to them on an artistic level, why regularly eviscerate their own work?
I don't see a violation.