Calling what the Pixels run "Stock Android" is a misnomer. Even being lenient, I'd argue Google's phones haven't really run anything close to stock Android since the Nexus 4. The Nexus 5 was when they dropped the AOSP launcher for one that integrated with Google Now to the left of your homescreens, replaced the default messaging app with Hangouts, and that was when the Google apps replacing stock apps really took off. Modern Pixels are certainly not running stock Android.