Accept builtin options with -D when making initial meson call

Currently meson only accepts `-Dopt=value` for builtin options when
calling `meson configure` and `--opt=value` for builtin options when
calling `meson` initially. This is a confusing behavior, and users only
get a small warning at the top of a potentially long configuration
summary to catch this.

This has confused end users and developers alike, there are at least 5
duplicates of the bug this fixes, and I have personally been asked about
this more times than I can count. The help documentation doesn't make
it clear that -D cannot be used to set options like prefix and bindir.

This adds support for -D options to the initial meson call, but not --
options to the meson configure call. I think it's better to have one way
to do things, and -- options are kinda one off while -D is used
everywhere else, so lets stick with that.

Related #969

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