If I understand correctly (sorry, not a Gentoo user), you’re saying that Gentoo is shipping the letsencrypt-auto version of the client?
The intention behind letsencrypt-auto was to provide a script that users who don’t have access to a native package through their distribution can use to install all dependencies and run the client. That’s why it does things like version checks and auto-updates (which you can disable using --no-self-upgrade) - a job that’s normally covered by your package manager. It’s essentially a stop-gap until all current versions of major distributions include the package natively.
Packaged versions of the client (as shipped by Debian, Ubuntu or Fedora) do not use or ship letsencrypt-auto and won’t auto-update. It sounds like the Gentoo package should probably do this as well.
On another note, I’m not entirely sure what you’re referring to with the regression you’ve experienced from 0.4.2 to 0.5.0. Are we talking about the fact that multiple <VirtualHost>s aren’t supported in the same file? Because that’s been the case from the get-go. I’m not sure about the <IfDefine> thing.