Configure: ensure that a DEPEND generates the correct inclusion directory

We incorrectly assumed that explicit dependencies meant that the
source directory would be added for inclusion.  However, if the
dependent file is generated, it's stored in the build directory, and
that should be used for inclusion rather than the source directory.

Reviewed-by: Rich Salz <rsalz@openssl.org>
(Merged from https://github.com/openssl/openssl/pull/5153)