Yes fauxfreshness, a very interesting and insightful post, thanks for sharing. IANAL, but with my limited exposure to legal stuff in this area, and the apparent fact that Josh Coalson began development of FLAC no later than 2000, I think that the risks of "Route of legal recourse and support" at least are manageable in the U.S. at this point. FLAC is supported in lots of paying software and to my knowledge none have been attacked by patent trolls yet, and with the 20 year limit from filing for U.S. patents filed after June 8, 1995, it would seem patent trolls might not see enough potential blood money to attempt anything worrisome. With fair certainty, any troll trying to assert a U.S. patent filed after 2000 will have a significant "prior art" issue.
Overall, Xiph (which has taken over managing FLAC from Josh) seems rather sophisticated and pragmatic in managing intellectual property issues, and managing any issue I've seen in general, so if MS was open to the possibility of natively supporting FLAC I'm somewhat optimistic a deal could be worked out. I would agree that the current support/development model for FLAC is sketchy at best (especially considering the personality of the lead person for FLAC development at the moment, but that's another story), but my gut says Xiph would provide a more robust support model with at worst a reasonable financial contribution to cover support and development costs that would be negligible to MS.
FWIW, FLAC libraries are apparently covered by BSD, but whether that's sufficient or not for enough of MS's concerns to make this worthwhile is beyond by expertise.
In short, while I think the "not enough paying customers care" could be the more significant factor, I'm hopeful the actual costs could be low enough that the downside risk is low and upside potential benefit is worth the effort. But I'm an optimist, so I could be wrong.
It would be cool for someone with the connections to try to connect MS and Xiph to explore this, noting my complete ignorance if this has been tried already. Is there anyone listening that could try to set up a "speed date"?