It is not so much an issue with the OS, more how the audio tracks are encoded.
I can not say that I have ever seen a native 2.1 recording and, as your 2.1 system uses a single TRS stereo jack, only stereo sound is outputted regardless of any settings.
The '.1' is just there to supplement the sound from your stereo speakers.
Yep you're right there, there is no need for a 3 channel sound system so instead the subwoofer amp splits the signal so that the woofers&tweaters handle left and right and the subwoofer handles everything below a certain frequency. There was no point for any software development as you're not using any extra channels. 5.1 and 7.1 is encoded with 6 and 8 channels in mind, and the same with 6.1 but as far as I am aware, 6.1 was still 6 channels, just the amp in the subwoofer is supposed to do the job for you and split the frequencies, much the same way a tweeter and woofer does in a normal stereo system.
I, too, noticed a lower quality in the bass when switching to windows 7. The best way I can find to correct the problem... In the control panel menu for "sound", with Speakers highlighted click the properties button. In the following properties window select the enhancements tab. Make sure the "Bass Boost" and "Virtual Surround" are both checked and Apply any changes. Then enjoy!!!