On one of the other forums, in YACT (yet another capo thread), something was mentioned that I had never heard of.
Tommy Emmanuel was showing how he uses a capo (midway between frets, I believe) but after he puts it in place, he presses his palm downwards against the strings at the soundhole (stretching them). And that really helps the intonation.
In probably an extreme case, I've tried it on my Taylor Koa 12 (K65ce) and it really helps. I use the 12 string Schubb capo (have tried many others) and that technique works almost all the time and certainly minimizes the intonation issues on the lower E pair. I do have the Taylor wave compensated bridge which may also be a factor.
I'd post the YouTube video but now I can't find it. As we all know, Tommy is amazing, not just from a technique standpoint but all the little tips he gives out freely are just great as well.