I think I understand the issue, but not its solution. There are more or less three standard ways to change faces now: Customize, themes, and use-package :custom-face. But there is no clear way to resolve the ordering between them, or whether they replace or inherit at each level. The behavior I was surprised by, and that has been reported previously, is that there was no way to specify a replacement for face settings. But Steven is surprised by the fact that things now happen at a level below theme application, and the theme replaces instead of inherits the defface spec.