The compression and eq in the amp sim will affect the response of the guitar and the distortion, if any, that the sim is giving you. EQ and compression after the fact is simply processing what came out of the amp sim.
For example, if you crank up the low end in the amp sim, you will end up with muddy distortion and the high end will be swallowed up by it. If you add an EQ after the sim and crank up the low end, it doesn't change the distortion, it simply turns up the low end on what you already had.
The same basic thing will happen if you put the EQ before the amp sim.
It's two completely different things.