I think it would be useful if we had an option when deciding to open a bounty on a question that we could choose to allocate rep from one site even though the bounty is being offered on another site.
For instance I would like to use my rep from SO for putting a bounty on a question that resides on SF. I don't have enough rep on SF to make it enticing. So when you click on "start a bounty" you get sliders for each site that you can pull your rep from, maybe make it where you need to burn up all your rep for the site that your asking the question on and then allocate more rep from other ones, if you have it.
thanks devinb for clearing up my question with your comments! " transfer rep INTO a bounty. But you can't transfer rep across accounts. So, the rep you'd 'lose' from SO would never actually go into your SF account, it would go straight onto a bounty on whatever question." – devinb