Seemant,

I'll follow up with one more thought...  The reason for the existence of
/etc/init.d, /etc/conf.d, /etc/env.d, /etc/cron.d, etc. is not to
arbitrarily split up configuration files into smaller sections.  It's
for a single reason: To allow the files to be installed by separate
packages.

Since /etc/make.conf is installed by a single package (portage, of
course), the logic used for the other /etc/*.d directories doesn't
apply.

Aron