I'd try to figure out a way to space it up from under the carpet, so it doesn't look like something's out of place at the bottom. Put some insulation or something under the carpet right at that spot to fill the void, and it'll be all good!
Have you thought about cutting out a piece of the stock console to fill in the gap? You might be able to use a strong glue to 'bond' it to the new one.
We bought some leather seats out of an 02 for Jess' car, and they gave us the center console along with them. I like the cupholders, so I thought Id see if it would fit, and well...