No real problem, because as you say you don't ride the combination anyway. As a matter of fact this is the standard fudge when the gear combination exceeds the capacity of the RD.
You cannot cut a chain shorter than the minimum length (large/large + 1") because to the off chance that you might shift into that gear accidentally, destroying drive train parts. OTOH, the worst thing that can happen with a chain that's too long is it sags a bit if you shift into the small/small, and you can correct that easily enough.
In some cases, I've retrofitted "bailout" grannies on road bikes when people were anticipating a hilly tour. I've had some where the grannie could only be used with the largest few rear sprockets, but it was an acceptable trade off to avoid replacing the RD.
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