It does change the date, but that also happens when you Pokéshift normally. Pokéshifting changes the date to the day you Pokéshifted - that's not a program's bug.
I don't see any problems regarding its legitimacy. It's like asking if a Pokésav cloned Pokemon is still legitimate. Of course, if you want to trade and dont want me to Pokeshift using the applet, just ask.
I'll take Gengar and Vaporeon. I'd like two copies of each; one for 4th gen, and one for 5th. If either/both are your OT, could you nickname one of the copies of each with a non-fully capitalized name? (i.e. "Gengar" instead of "GENGAR") I'll be online to trade in a few minutes.