Just bought a 2nd edition SE from Apple and was also charged the Verizon $40.00 "One-Time Upgrade Charge". Most unfortunate because they're charging me for something I can take care of myself by simply swapping my existing SIM card from my old SE into my new SE.
I did this when I bought my 1st SE but at that time, I had paid full price while at an Apple Store. Switching the SIM from my iPhone5S, Verizon automatically recognized my new phone with no upgrade charge. In fact this was recommended by the Apple sales person. I will take this up with Verizon but I'm also disappointed that buying an iPhone through Apple resulted in what I view as an unnecessary charge. Perhaps this is what Verizon demands from its customers when dealing with Apple.