You've missed out another benefit (of Gentoo specifically): the ability to conveniently apply your own patches – just copy them to /etc/portage/patches/category/package-version and then re-emerge the offending package.

Most users will probably never need to do this, but I find it invaluable.

I maintain my own patches for dozens of packages in order to fix quirks/WONTFIX bugs, add features that upstream refuse to touch, remove intrusive/unwanted features that piss me off, etc, and being able to do this without also having to maintain my own deb/rpm/<some other package format> makes it much less painful.

It's also nice for applying emergency security fixes without waiting for your distro to pick them up.