Re: Hmmm...
I think when they say "software overlay" it's just a custom launcher/homescreen APK... All you'd need to do is get the stock Launcher.apk from somewhere - install it, then Android will say "Which Launcher do you wish to use?" and you pick the one you've just installed...
Of course that's for now anyway. Although even previous Nexus builds weren't totally stock android (AOSP+GApps) anyway, with their HP print-malarkey apps etc.
Interestingly, no-ones said whether the Pixel phone will still come with a bootloader that you can unlock should you want to, as the Nexus devices did... I wonder if they'll release a "Developer" edition of the Pixel phone with a build of android that comes without the Pixel-specific launcher etc. and with an unlocked bootloader - a few months down the line?