Probably because the Gentoo ecosystem (package tree, package managers) is build for source packages and not for binary packages.
ChromeOS/ChromiumOS uses portage for its build system, to produce a signed, read-only image that the OS can boot from. CoreOS uses the same tooling FWIW: http://www.chromium.org/chromium-os/build
This is why you can’t just install random packages onto the parent OS. Any additional software needs to run in some overlay filesystem or sandbox.
Package managers which are build for source packages (e.g. ebuilds/exheres) have a much more complicated logic running in the background, come up with much harder to solve problems and are a lot slower (orders of magnitude).
The only aspect where this setup is superior than e.g. arch + pacman is when it comes to using source packages on the same system. So I guess that is nothing you would like to use on a Chromebook anyway. Therefore, using a Debian container is a reasonable choice, in my opinion.