You have one menu for the whole application as well, but some options will be enabled/disabled when you switch between documents (e.g. one layer doc should have "flatten layers" option disabled).
In real life if you have two easels, one for sketching and one for oil painting and for some reason you prepare both pieces simultaneously, you definitely don't want the same tools for both. The fact that you have one tool dialog does not mean you should stick to one active tool, color, etc. per application. From my point of view - tool and color assigned to document is more intuitive (although most apps have them common for all documents).
But still, it's your decision.