I thought this was something only I was having an issue with. My Notch has done the same thing as long as I've had it. I've been through countless exhaust setups, verified over and over that there's no leaks ANYWHERE along the exhaust from the block to the tips, and I've sealed and re-sealed the trunk weatherstripping, all to no avail.
You're probably on the right track, thinking that the windows being down does create a vacuum that pulls the exhaust from the back to the front, but there's probably more to it, I'm sure. There's this low-pressure swirly area of air following your car while you're moving forward, this pocket of exhaust fumes that gets trapped back there, and it seems to find every little crack and crevice available to suck back inside a Fox.
My Notch does it, Frankenstang's Capri/Hatch does it, and my buddy's pristine '90 Notch does it, too. It's always particularly obvious when you really romp it to WOT - if you're running off-road pipes, you get a nice stink of that unique-smelling raw exhaust. Every time I'd drive my Notch home from work at night a couple of years ago, my (now ex-)girlfriend would greet me with a hug, sniff me, and say, "Ewwww, you smell like cars."
I'm not sure if there really is a way to cure it. I've tried running full tails, dumps, and side-exits, I've tried siliconing every seam I can find, I've re-weatherstripped the trunk, etc. ... doesn't matter if the windows are up or down, there's always a stink. I just try to keep the sunroof open as often as possible to let it vent out so that it doesn't build up. I used to actually get a buzz there for awhile when I was running side-exits, in fact, because it used to recirculate so badly. Not good when you're running 70+ MPH on the Loop 202...