Generally it depends on who you work for. I'm with UA, and while we don't have agreements in F for either airline (for that matter, I'm not sure if we have agreements with Virgin at all, I know we don't with AF) we do with many Star Alliance carriers. But I think outside of that ecosystem, it's quite rare.

Bottom line: look where you order a ZED fare. If you can't get a ticket in first or business, you probably can't sit there. But if you're lucky, they may upgrade a revenue passenger to make room for you in Y. I've heard that is official policy for Lufthansa, for example.