I agree. Sometimes someone can't drive manual or doesn't want to for any number of reasons, and because of that, they miss out on certain features.
Personally, I've always wanted manual in a Mustang, but since we already have one with manual, if we were to ever get a second I'd want automatic. For a few different reasons.
And the more that I think of it, why would Ford want to not make some options available? It would be more money they'd get. They'd get the $ people pay for the automatic, in addition to the $ they'd get for the Brembo package, or whatever option may be in question.