When writing a file, creating a new inode has some clear advantages: 1) existing files can be replaced atomically with os.rename() 2) leads to copy-on-write behavior with hardlinks, which is useful if someone wants to use hardlinks to create copy-on-write repository snapshots on a filesystem such as ext4 (no need for btrfs or zfs)
A fix for egencache --write-timestamp is now in the master branch: https://gitweb.gentoo.org/proj/portage.git/commit/?id=4ec443f2ac57040304107720f24cad6b4651c7a4 We still need to fix --update-use-local-desc and --update-changelogs.