I'm working on a patch to fix this.
Actually, it does work with repos defined in repos.conf. I just needed the --overlays option. Anyway, I'm working on a patch to migrate away from the deprecated PORTDIR_OVERLAY variable.
Created attachment 439476 [details, diff] eshowkw: migrate to PORTAGE_REPOSITORIES
Thanks Zac. Patch looks good.
This is in the master branch: https://gitweb.gentoo.org/proj/gentoolkit.git/commit/?id=84aa6c743581222a3f4a8a855dbcb77a2774c5b6