Do an product need to be intact to count? If this is the core of Monsanto argument, then it sounds to me as completely rubbish and something a court should have no problems throwing out.

Lets say I bought a new mousetrap. After purchase, I go around and add/remove aspect of it. I change the color scheme. I change the cheese to a more smelly version. Has it now suddenly become a new mousetrap and is thus no longer the same physical object as first sold?

If the seed still embodies the details described in the patent, how is it not still the same object? I could understand Monsanto counterargument if no aspect of 1G seed existed in the 2G seed but thats of course not true. More likely, all patented aspect of 1G seed is all still in 2G seed. If that was not true, than even if Monsanto won, they would loose as they then would have no claim on 2G. Thus the only changes of 1G -> 2G must be trivial and not covered by the patent.