Meanwhile I found this:
Gentoo Forums :: View topic - os-prober creating duplicate entry for main linux system
TL;DR
a partition can be blacklisted from os-prober so it doesn't show up twice
perhaps on EFI there's no need for a GRUB entry, but I don't have EFI and don't know jack about it.
edit: posting this just in case someone is still on BIOS booting, my previous comments were due to my misunderstanding that this case is about an EFI boot.