native packages that are going into the sysroot should install the schema files to the prefix as usual, not run gconftool at install time (by exporting GCONF_DISABLE_MAKEFILE_SCHEMA_INSTALL), and then use SSTATEPOSTINSTFUNCS to run gconftool when the sstate is installed.
I originally filed this more as a "it should" than "it must". My recommendation (with a bias as I'm the assignee) is to drop the priority of this to low as we don't currently have any native packages that use gconf.
GConf is now mostly dead so this is pointless.