OS X uses /usr/bin/manpath to construct the MANPATH on the fly. If you set the MANPATH environment variable you will not "see" your other man pages unless you explicitly set them in the MANPATH (unless you invoke man -M command).

/usr/bin/manpath will construct the MANPATH based on directives in /usr/share/misc/man.conf and your PATH environment. If PATH contains /opt/local/bin and /opt/local/man exists it will be added to MANPATH.

Your comments are informative and a helpful warning but the "Don't" in the title seems too strong since there can be valid reasons to explicitly set MANPATH instead of modifying /etc/manpath.config.

Maybe you don't want to (or can't) modify manpath.config and would rather set MANPATH than run "man -M path ..." commands. You could use the output from "manpath -d" as the starting point for constructing a customized MANPATH, keeping manpath.config generic so there's no risk of an local customizations you've made to it being clobbered by an Apple update (although quite unlikely for that particular file).