I don't think that's how manufacture warranty law works.
If this is true then iFixit could be held liable for faciltating and encouraging it with it's adhesive strips and repair/upgrade guides. I think Apple would have to prove that the repair or upgrade work actually caused any issues not just using it as an excuse to deny warranty coverage for a known issue with that model.
If someone purchased a new car and expertly disassembled it and then reassembled it would the manufacture be able to deny warranty coverage for an issue that was affecting many of the same model cars that had not been disassembled and reassembled. I don't think so. If the car had been modified and that modification plainly caused some sort of failure then that cause and effect would not be covered. If there was also an issue unrelated to the modification I doubt if the car manufacture would be able to deny warranty coverage for this issue because of the modification.