From what I understand, yes there are some differences. A flashed card in a Mac Pro can used only one DVI port, so if you want to use a second monitor there can be issues, I could be wrong on this, but I believe it is the case. Some cards have issues on boot up where there is a grey screen for a few seconds before it boots into OS X, again not sure if this has been resolved.
I considered a flashed card but then decided I didn't want to risk having issues down the road, and paid the extra money for a proper Apple video card. You may never have issues down the road, but you are essentially fooling the Mac by using a flashed card, so I think its hard to say there may not be issues with future updates or Lion.