Canonical way to set compile flags with package manager

[Harry Putnam <reader@newsguy.com>]

If I wanted a special compile time flag set at compile time, for a
package, is the only way to just compile it myself, or is there some
procedure where the package manager is involved and thereby is able to
keep stats on the installed pkg?

For example:  I keep a fair number of system files, like etc/hosts
etc/fstab, etc/rsyslog.conf and etc etc. under cvs to track my
experiments and to be able to easily recover a specific version of
some config file when needed.

I want cvs to be compiled with --enable-rootcommit.
I find it much easier to manage permissions on system files that are
in use but are still under cvs, as root.

Its a single user system so all commits are by me.  And so any
user name that shows up on a commit is really me.

I went ahead and compiled it myself and installed in /usr/local

Is there anyway to do that and still allow pkgmanager to keep track of
the install?