It confuses people if equery to not list an ebuild in the portage tree if a similar ebuild do exists in the local overlay (https://bugs.gentoo.org/show_bug.cgi?id=330485#add_comment) Reproducible: Always
I think no. `equery list -p -o' lists installable entries. By default (that is, without masking either the overlay or the official "gentoo" repo), ebuilds (with the same version) in overlays are preferred over ones in the "gentoo" repo. So `equery list' accurately reflects what is available in the tree and in overlays - the one in the official tree is overridden by the one in your overlay. Still assigning, because maybe it could be extended with a command line option that reveals same versions across repos.
Actually, this is now do-able after some changes zmedico and I had made to portage for eclean which will allow code to specify the trees to look at. It still takes looking at all trees to find them, but do-able.