The trouble is that multi-column FKs are not handled well by the diff code regardless of the database type. Improvements to diff (including multi-column FKs) are the focus of the next release which I’m hoping to have an initial beta of within a week or two.
I’m not sure I know of any workarounds off hand besides manually updating the generated XML based on how you know it should be. I’m not sure how you are using the diff to know how do-able that is.