Staples specifically sells VGCs as well as MCGCs along with routine GCs from retailers. So I am not surprised that Amex gets level 2 data.

However, in the scenario that you describe, you buy, for example, a computer and Newegg sends you a $50 VGC, I highly doubt that the information sent to Amex would include the fact that you received a GC bonus for buying the computer. Maybe what you are talking about is different than what I have just described.
However, nothing surprises me anymore so if you have information to the contrary, I'm sure we would all like to see it.