Re: can't set both mode-line color and default frame font?

[Richard Stallman <rms@gnu.org>]

    Only if you say it does ;-). That's just repeating the assertion that
    `custom-file' (Emacs Lisp) should take precedence over X resource. The
    question is "why should it?".

There is no general theoretical reason why Emacs face customizations
should take precedence over X resources.  Sometimes users want that.
Sometimes thy want the opposite.  But nobody has seen any general rule
for figuring out which one the user would prefer.  Unless we add
another complex feature for specifying which -- and that doesn't seem
worth while -- we must adopt and document one choice or the other.

Of the two choices, having face customization settings take precedence
seems better.