the factory crossover will filter out all the high frequency sound out and send it to your factory dash tweeters.
He's right. Your 6x9s won't get any high end signal, because the xover will send it to the pillar tweets...effectively making the tweets in the 6x9 useless.
I think the pillar tweets sound like crap compared to the tweets in the aftermarket speakers. They sound like air hissing through a leaking box...and very dirty at high volume. It's your system, but you'll be hard pressed to get people to agree with the idea that the stock tweets sound good when you have components/coaxles in the doors.
-sky