There is not AFAIK a public method. A less-fragile workaround instead of relying on private API might be to first resolve with your source object in there as a fallback, then iterate over the keys in the source object you resolved from and just remove those unwanted keys from the target object.
I can't think of a reason not to add a Config.resolveWith(), though I wonder if there was a reason since I do remember considering it. Maybe I just figured nobody would use it.
If you do a pull request, be sure to include tests and docs. I think the pull request is reasonable, assuming it turns out to be very little code (as I would expect). The current master branch is open for API additions, to appear in an eventual 1.2 release.