There's some information available on developer.apple.com, although this particular page is more geared at Sticker Pack creators: https://developer.apple.com/app-store/sticker-submissions/
* Do we need to create a separate "app" in iTunes Connect? If so, will these "app extension-only apps" also show up in the regular app store?
For standalone iMessage apps (which I include Sticker Packs in this "iMessage app" designation), yes, you would create a separate app in iTC. If your iMessage app is being bundled inside of an existing parent iOS app then you wouldn't do that (the iTC app would be for the parent app).
* It's possible to bundle Messages app extensions within a "normal" iOS app. Will Messages app extensions bundled in this way show up in the "Messages" app store?
* If we distribute our Messages app extension through both distribution mechanism (ie. bundled with a normal iOS app AND as a separate app for the Messages app store, should both copies of our Messages app extension use the same app bundle id?
You should pick one or the other approach. Either do it as a standalone iMessage app, or bundle it in an iOS app. Don't do both.
* If a user installs our Messages app extension through the Messages app store AND installs our normal app (which includes our Messages app extension in its bundle), will the app extension show up twice in Messages? Will these two copies be upgraded separately?
Per the above point, you should only have one or the other. If you already have an iOS app it probably makes most sense to add an iMessage extension to that existing app. Installing either through the iMessages app store or the normal iOS app store, users will get both installed.
Thanks, pdm, this is great info. However, there's one question from the original post that I don't beleive has been answered:
> ... will these "app extension-only apps" also show up in the regular app store?
I have an "app entension-only" app, but I'm concerned that I'd be missing out on a major opportunity for discovery if the app isn't also listed in the regular app store. I'm tempted to bundle the extension with a simple "regular" app so I can be sure that it's listed in both stores, but that's not ideal. (And in this scenario, would App Review judge the standalone app on its own, in terms of providing useful content, apart from the bundled app extension?)
Since it's difficult to switch from "extension only" to "app with extension" after the app ships, clarity on this point would be greatly appreciated.
One more question please, does that mean we can submit now? I remember reading in here in the forums in another thread that developers will receive an e-mail stating the opening of the iMessage app submission.
If we can start uploading apps now, what is it like, just go in iTunes and make a new iOS app like the very classis app store app submission?
No, submissions of iOS 10 apps are not currently open. You can submit iMesage apps and sticker packs to Test Flight which is largely the same as submitting to the App Store since those go through review, but you cannot submit to the real app store yet. I do not know when submissions will be opened up, but we'll surely communicate this to developers when they are.
According to _davidsmith on his podcast Under the Radar - what happened last year was that iOS 9 Gold Master was released after the Apple media event and iTunesConnect took submissions around 10PM PT.
Past events do not indicate future ones - but this is my assumption, trying to submit my Apps on the evening of September 7 (confirmed day of Apple event).