"and the interaction between the three drivers would probably be a huge mess!!!"
Not as much as you might think, Bufus. The stereo sub pair act as simply another driver added to each of your front speakers, since they run off exactly the same signal as the left and right front speaker. It helps if the subs can be placed pretty near the left and right front speakers, as well. Using a pair of subs, as opposed to a single sub can help greatly with some room node problems. Additionally, I disagree with setting the pre/pro for no sub since that silences the LFE or ".1" output. While that method will function, it forces digital re-mixing of the discrete LFE channel by your processor which dumps low frequency info back into all five other channels, which isn't a good thing.
"because the ".1" channel (subwoofer output for "5.1" system) will contain frequencies that are too high to put into your subwoofer."
Uh, not unless your processor is really screwed up. This channel won't contain anything in the setup that you describe...it will be off. And even when it is on, it will never contain frequencies higher than the crossover setting in your source or pre/pro which may or may not be adjustable and is almost always somewhere between 35 and 150 Hz.
Everything else you had to say, I agree with. Good point about the Y-adapters...I completely forgot to mention that possibility. You make an INCREDIBLY good point about where to set the sub crossover for best integration, as well. I do the same as you in crossing over my stereo subs at a very low frequency, specifically about 10Hz below the lowest frequency the main speakers can produce while still having a flat in-room response. That way, when crossover slope is taken into account, I get a very smooth transition. Obviously, the exact number of Hz below to set the subs would depend on the slope of the sub's crossover and would have to be increased in the second scenario I mentioned, using an outboard crossover to relieve the main speakers of some of the low frequency info, but you get the idea. I'm glad to see I'm not the only one who found they got the best results that way. I do set the LFE channel sub higher though, at around 100Hz, to get the most slam for movies then turn the crossover down for those rare instances when I listen to multichannel music. At least I only have to mess with the setting on one sub, though. The stereo pair stay right where they are set regardless of the source...two-channel or multichannel.
"Wow, the advice about using 3 subwoofers sounds VERY expensive"
Well, it can be. Maybe that's why I'm...