haemphyst,
While you might not be able to say, "you have 2 12"s and 2 10"s," won't the sound be slightly muddied without the help of some time delay, variable phase, eq, or some combination?
Now, maybe I'm totally off-base - physics was more than a handful of years ago for me and I've just recently become highly interested in audio. But here are my concerns with different drivers in different places in the car anyway... Please feel free to knock my thoughts down at will, I am honestly curious::::
I don't think the fact that the actual cones are larger gives me pause, rather, I am concerned with the different motors, different enclosures Q?, and locations.
1) Delay caused by different motor inductance numbers
2) Delay caused by different locations
3) Different enclosure Q's
1) Different motors, with different inductance numbers (thanks Steven), will have different transient response characteristics. In other words, woofer 1 will be firing slightly ahead of or behind woofer 2. Even if located in similar positions in the vehicle, wouldn't this cause a slightly muddied sound? Won't one woofer be settling slightly behind the other? Won't this lead to slightly looser sound as the beginning and ends of signals will be playing supported by a single woofer rather than two?
2) Our friend AJRXtreme talks about placing his low frequency woofers in two completely different locations. One set located very close to him, another located relatively far away. Won't this difference cause some noticable time / phase / cancellation problems? Now, I realize the lengths of the waves are very long. But won't the close set arrive at our friend's ears significantly prior to the far set? Won't this cause the same sort of muddiness or bloat that I have a hunch would happen above?
3) Different enclosure Q's. Different motors have different T/S parameters. Unless care is taken to match the enclosure Q's (or at least get close), won't this also cause differing transient response behavior? One speaker might be rather tight, another boomy? One having greater extension, the other more peak? Cabin gain exists because the bass notes stay in the car, even though the waves are very long, won't SOME cancellation related addition and subtraction occur?
Playing pink noise or a sweep, you're right .. these considerations probably wouldn't have much effect on frequency response. None of these considerations will probably matter to most people, especially those just interested in SPL. However, one thing I'm slowly learning as I research speaker building more is that overall sound quality goes beyond just the frequency response graph.
Also, some of these things can be corrected for with some of the features on DSPs and some analog signal processors. Others can be taken care of by switching the phase 180 degrees or taking care to obtain similar box Q's. When someone comes here asking though, shouldn't we warn them that different sized woofer in different locations playing the same frequencies is probably not ideal for sound quality? I mean, we can still tell him/her to go for it, but shouldn't they know that it isn't the recommended path for sound quality?
Again.. please comment, I'm in a learning process here and wouldn't be surprised if most of these were wrong or don't matter. 
New Project: 2003 Pathfinder