Am I right to assume that the current implementation requires the scrollable element to exactly fill the viewport? And if so, what is the rationale for this decision?

The explainer does not define any requirements for the root scroller: https://github.com/bokand/NonDocumentRootScroller/blob/master/explainer.md

Please see the attached image. It is intended to illustrate a sitatuion where the scrollable section is positioned underneath the app-bar (so that the scroll-bar doesn't overlap it). In this example, my expectation would be for the scrollable section to be a valid rootScroller so that rubber-banding (or "glow") will appear from beneath the app-bar rather than the absolute top of the viewport. Will this behavior be supported by the current implementation?
This is something I think will help bring PWA's even closer to their native counterparts.

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> The explainer does not define any requirements for the root scroller: https://github.com/bokand/NonDocumentRootScroller/blob/master/explainer.md

It's a bit of a footnote in the "Proposed API" section but it is mentioned. The rationale is that it makes implementation easier and punts some of the hard UX decisions (i.e. how do we "expand" the root scroller if it doesn't fill the viewport, how do we show scrollbars when user pinch zooms, etc). See the updated https://github.com/bokand/NonDocumentRootScroller/blob/master/howto.md for more details.

The decision is preliminary and meant to get this feature out sooner. Restrict and loosen based on use cases is a lot easier than launching a very general solution, finding out some aspect of it was a bad idea, and trying to restrict it.

At first glance, your use-case seems like a natural follow-on so I think it'd make sense. Though I'll need some more time to think about it and possible consequences. 

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