apps/{ca,req,x509}.c: Improve diag and doc mostly on X.509 extensions, fix multiple...

apps/{ca,req,x509}.c: Improve diag and doc mostly on X.509 extensions, fix multiple instances

This includes a general correction in the code (now using the X509V3_CTX_REPLACE flag)
and adding a prominent clarification in the documentation:

    If multiple entries are processed for the same extension name,
    later entries override earlier ones with the same name.

This is due to an RFC 5280 requirement - the intro of its section 4.2 says:

    A certificate MUST NOT include more than one instance of a particular extension.

Reviewed-by: Tomas Mraz <tmraz@fedoraproject.org>
(Merged from https://github.com/openssl/openssl/pull/13614)