The OS is otherwise the same as what you get on a Nexus.
This was the crux of my post - it's not at all the same. It looks and feels very similar but the actual framework is entirely different. One difference would be enough to be different and there are hundreds. It's not stock with a different kernel, it's closer to more accurate to think of it as Sense or TouchWiz camouflaged as vanilla. I really don't like telling people to go search, but this is something that can be researched. Just AC's podcasts and blog posts are enough to highlight some crucial differences.
Props to all involved for making the deception so convincing. Of course, that's mainly due to some much stricter guidelines of how those devices will look and feel, but it really is hard to tell without noticing the aforementioned clues... ie features that are not hardware dependant yet are included in GPE devices but not on Nexus devices. That and the explanations by the blog staff of AC and other sites. I don't pretend to be an expert on Google's coding practices and the minutia of firmware politics, but I do like reading it and I generally do trust the actual experts.
Android has supported hardware home buttons before, so I don't consider this a deviation from stock.
Support for physical *navigation* buttons has to be added in and is technically a violation of the design guidelines. It hasn't been included in the source since the end of 2012. It's not a foreign concept, but it's foreign code.
It's not something that is introduced by a vendor skin.
Physical buttons are supported, such as volume and power. Physical navigation buttons are not supported and that support is added by the OEM.
So IMO, GPE devices are just as vanilla/stock as the Nexus is.
I could buy into an argument that they're both different from AOSP and thus if we think in binary terms, they are not stock. But they're also not the same as each other. The analogy here is that neither you nor I are Marilyn Monroe - but that doesn't mean we're the same person.
SD cards are stock Android as well...Android includes support for SD even though Google stupidly and pointlessly left it out of the Nexus.
SD cards were not until Kit Kat directly supported since 2011. Now that they are supported, it's a moot point, but in any case Samsung's implementation was completely different than how they were read by other Android devices prior to Kit Kat. Now they're much more similar. And since there is official support with Kit Kat and the future L release, we may see cards included in Nexus devices. Regardless of the future of SD cards, the S4 GPE uses Samsung code native to the Galaxy S4 (touchwiz version) to support that feature.
And the exception to all of that stuff is the Moto G, which was - due to Moto's very near stock implementation - so close to stock that removing Moto's customizations essentially makes it a very closely related deviation from the Google line.
The differences are mostly all below the surface, but not caring about them doesn't make those differences not exist. I'll fully admit, to 99%+ of consumers, the differences would be nearly invisible, but that doesn't mean they actually are the same.
I suppose if we really want to hash this out, we can create a thread on the differences between GPE and Nexus devices.