pkgbase: hide duplicate METALOG directory warnings under verbose

Creating directories multiple times is an inherent side effect of the
way installation is done. Hide warnings from duplicate directory
entries (with identical metadata) under metalog_reader's verbose mode.

Duplicate file entries are always reported. They currently generate
warnings but will be switched to errors once the few instances currently
in the tree are fixed.

PR: 244596, 271178
Reviewed by: kevans
Sponsored By: The FreeBSD Foundation
Differential Revision: https://reviews.freebsd.org/D39898

(cherry picked from commit 2a3bd0870869819354b5ea65761d13e5e2987697)