He points out that if the nirmankāya and Sambhogakāya were the same continuum, then when the Buddha stepped on an acacia thorne, Vairocana in Akanistha would have been harmed. He therefore, states that the relationship between Sambhogakāyas and Nirmankāyas are like that of illusionists and illusions. However, what he was referring to was puppet shows, since that is actually the kind of illusion being discussed in that example i.e. taking clods of earth, sticks and so on, and causing the illusions of people, elephants and so on to appear on a screen.
Where does Gorampa discuss this?
Gorampa's argument is not really logical (that must score max points for some kind of combination of irony and arrogance on my part) and is constrained to a particular interpretation or sets of interpretations. Your paragraph explanation can be debated but ..... well, I lack the background to debate this seriously.
If considered seriously a nirmanakaya as a *puppet* is problematic on many levels (for one thing this can be seen as denying liberation at the level of Buddhahood). As an emanation and thus a kind of illusion (but not a puppet) this is not problematic.
Even the case of Shakyamuni is problematic with this puppet interpretation while attaining full enlightenment in the remote past and then enacting (or playacting) the twelve deeds isn't.
_________________Kirt's Tibetan Translation Notes
"Only you can make your mind beautiful."
HH Chetsang Rinpoche