[@Mtntopview]
Considering that's about as far from canon as you can get, I would estimate that the only reason it had the effect it did is because of bad writing, and nothing more.

However, if dark energon were to function by that rule, it would most likely infect Apocalypse. However, as Apocalypse is nigh-indestructible, and a force of evil, and the Dark Energon seems to possess some measure of intelligence, it is more likely to attempt to turn him into a user than it is to inflict any harm on him. If it did become harmful, I doubt it could do much before Apocalypse adapted to it and became immune.