All of the Windows shell supports UI automation, so if you run into corner cases like this that aren't scriptable, you can just use PowerShell to automate the clicks.

Is this a thing you have to do often enough that its worth bothering to automate? I'd set it that way once, and its done, never have to touch it again.

The more inexplicable thing is why the modern/metro/universal/whatever-it-is-this-week apps don't show up in the volume mixer at all, and you have to rely on third-part tools like EarTrumpet to tweak them when they are being obnoxious.