I think that's an excellent point about Austen's idea of good breeding, and there's a scene in Pride and Prejudice that comes to mind regarding this subject. It's in chapter 45, when Elizabeth is visiting Pemberley and is received by Miss Darcy and the Bingley sisters:

By Mrs. Hurst and Miss Bingley, they were noticed only by a curtsey; and on their being seated, a pause, awkward as such pauses must always be, succeeded for a few moments. It was first broken by Mrs. Annesley, a genteel, agreeable looking woman, whose endeavour to introduce some kind of discourse proved her to be more truly well bred than either of the others...

I think that inversion of good breeding as having more to do with true consideration for others than one's birth/status/outward behavior is definitely a theme in Sense and Sensibility as well. There are shades and degrees of good manners - like you say, Mrs. Jennings does frequently make people uncomfortable with her open and joking manners, while Mr. Palmer does the same with his reserve and attitude towards his wife. But Austen is clear that both of them are capable of a generosity and kindness that we don't witness in some of the technically more polite people like Lady Middleton, so I think they do come across as the better- bred. Virtue always wins out with Austen, but it seems that her best characters are those that combine virtue, sense, and good manners.