Apparently the latest beta (10.12.1) has support for this natively.
https://github.com/tekezo/Seil/issues/68#issuecomment-250195...
https://github.com/tekezo/Seil/issues/68#issuecomment-250195...
I was using Karabiner to set caps lock to control AND escape when pressed independently, something extremely useful to use Vim and command line. This doesn't appear to be supported, unfortunately.
I really did not expect Apple to finally fill this gap that has been around for so many years.