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I've run 42T cassettes for a long time on Di2 and we've both run road Di2 on gravel bikes. There can be some chainslap but you'd have to big fangin' in the smallest cog and suddenly stop pedaling. It's basically a non-issue. If it's a consistent problem it sounds more like the seal thing mentioned, or maybe something needs a clean - like you've over-greased the freehub or something and it's sticking a bit too much.
It's almost surely the seal of the freehub dragging, nothing to do with chain length.