Yeah, the stage3 gentoo used for build sabayon/base uses new gentoo profile with separated dirs for /lib, /lib32 and /lib64 and the same for /usr. The same issue is the same that had generated problems with calamares.
Here, I think we need to check that chroot doesn't use links for /lib and /usr/lib and rebuild packages that have file under /usr/lib, /lib. FWIS there are packages with only files cross arch that could be maintained under /usr/lib but are few.
The second issue that generate broken links is the upgrade of the packages with changes in libs path as I saw for systemd.
My script (sabayon-brokenlinks) fix this last. But maybe fix also the issue shared by you. Probably we could find the packages to recompile with a script that use qfile. I will think about it and let you know.
My cent.
Thanks for the report.
geaaru