This is very poorly documented!
And since I just went multiple rounds with developer support until I figured this out (I'm not sure that developer support understands how confusing this is...) I'll share what I learned:
1. When you create a new Watch App project (not an iOS App with Watch App), note that it creates a Watch App target, a Watch Extension target, AND an almost empty iOS App target (no code, storyboards, xcassets, but under build phases it is dependent on the Watch App and embeds the Watch app).
2. On App Store Connect, you create a new iOS app project for your independent Watch app, but only fill in the data related to the Watch part of the project.
3. Archive and upload your project as you normally would a standard iOS project.
Voila! (And yes, that is not intuitive).