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From: Richard Stallman <rms@gnu.org>
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Subject: Re: customize
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      Thus
    my own config can't control the face, because customize insists on
    having the last word (and saying: suppress this face)

I don't understand what you mean, "saying: suppress this face."  Could
you explain more precisely?  This may be a very simple and localized
bug, but I can't tell, because I don't really understand the scenario.

What does (custom-set-faces '(trailing-whitespace ((t nil)))) do?
What is it supposed to do?
What settings did you specify in customize for that face?
You said "turning off the configuration option for it"; what does
"it" refer to here, and which option is that?