Counter theory (IANAL): My use of your software does not constitute acceptance of the EULA. If it did, no one would bother with having users click to accept the EULA. Instead, if I don't accept the EULA, the software is supposed to quit out. If it doesn't quit out when I click "No I don't Accept", then you're letting me use the software even though I haven't agreed to the EULA.
In this case, I the user am not clicking "No". Instead, I am replying with, "Yes, but with amendments." If the software quits out, fine. But if the software proceeds to let me use it, that sounds an awful lot like the company accepting the amended EULA. Your comments about the machine not being capable of processing and understanding the amendments is curious --- most of us users aren't capable of processing and understanding the original EULA, even with time taken to read through it. I would find it reasonable to say that the same standard of "opening the shrinkwrap" would apply to "allowing the user to proceed to use your software."