I was having trouble finding the node for this, thinking there was a flatten layer node.

After digging for a while I found the feature buried on the configure layer node.

My stumbling search led me to wonder if a toolscript shortcut would be in order.

Is configure layer the right tool for this?

The Merge node can also do this. And you can have the USD ROP do this at save time. It is an operation currently relegated to the Configure Layer LOP because it's not a concept that I think most users would want front and center as it's own tool. Certainly studios with a well defined layer structure wouldn't want users doing this ever… As always, I'm prepared to be talked out of this position, but that's my thinking on it (and of course you can always create your own tool if you find yourself doing this all the time).

The use case I can think of is if you sublayered bgeos or alembics and wanted to write them as usd layers and not just layers that say ‘sublayer x.bgeo’

Yep, that's exactly the kind of layer-structure-destroying edit that I was referring to that should not be exposed to every artist