Maybe it's because the same updating mechanism is used for both, but according to a thread in the Microsoft answers forums, those running Windows 10 Home will get Windows Store app updates in addition to regular Windows updates without the ability to turn either of them off.
The thread, appropriately categorized under the heading of Disable auto update app in windows 10, details a discussion about how the Windows Store setting for Update apps automatically is set to ON and grayed-out.
The thread takes an interesting turn when the Community Moderator, Smittychat, suggests that this option might be fixed with a schedule update in September and just check again then.
The exact response was...
I believe there is a scheduled update to Windows 10 RTM scheduled for September. It's to deliver a more polished build. Check Settings > Windows Update > Advanced Options to determine if the options have changed after September.
Later, after further discussion, Smittychat concludes with this…
Because these builds have been coming through Windows Updates, Microsoft had sent out a message that Windows Update settings could not be touched. It appears this goes for apps, too.
We've known long before Windows 10 RTM'd that the different editions of Windows 10 would update differently. Home users are on the Current Branch. As stated in the Update Servicing Branches Available for Each Windows 10 Edition article…
For home users, updates will deliver through Windows Update as they are released. This means that home users' PCs and devices will be the most up-to-date Windows editions on the planet. Home users will be constantly secure and will be able to use newly released features immediately. Security Updates, Features and Fixes are automatically applied and there is no option to delay or customize the updates.
However, even then, there was no mention that Windows Store apps would follow the same updating routine or be part of mandatory updates – only security updates, features, and fixes – and I'm not sure Microsoft ever stated it that way, either.
I have four systems running Windows 10 right now, but only one of them has Windows 10 Home edition running. And, I can confirm that only the Windows 10 Home edition has the option grayed out. So, it's not a bug as I thought before, but a feature. However, in my case, it was a bug. My Windows 10 Home edition PC (HP Spectre x360) was grayed out, stuck to the ON position, but the apps were not auto-updating as they should. However, I can also confirm that this has started working after applying the cumulative update 1 (CU1) released on August 5.
CU1 comes with a few new quirks, but overall several existing bugs I was experiencing are resolved and performance for things like Microsoft Edge have improved. You should definitely apply this if you haven't yet. Of course, if you're running Windows 10 Home edition, you have no choice.