I don't know if this is a bug or desired behaviour.
Having a custom /etc/site-config.jam "hides" /usr/share/boost-build/site-config.jam installed by boost-build and with it the variant gentoorelease defined there. Emerging dev-libs/boost-1.52.0-r5 (and probably also 1.49.0-r2) fails early in the process with
notice: could not find main target gentoorelease
don't know how to make gentoorelease
Maybe the ebuild could issue a warning that a custom /etc/site-config.jam is not supported or that the contents of the version installed by boost-build has to be merged into it.
+ 28 Apr 2014; Sergey Popov <email@example.com> boost-1.52.0-r6.ebuild,
+ boost-1.53.0-r1.ebuild, boost-1.54.0-r1.ebuild, boost-1.55.0-r1.ebuild:
+ Add apropriate die message on unsupported overriden site-config.jam, wrt bug
+ #456792. Thanks to Raimar Sandner <gentoo-bugzilla AT 404not-found.de> for
+ reporting this issue