Tomas Doran pointed out the other day, in a post on the Catalyst mailing list, that you could manipulate the session data between test calls if you needed to.
My original question was about manipulating what user was logged by playing with the cookie cache, but it should apply to any value in the session. You could check them, to see that the internal state of your program is what you think it is, or you could fiddle with them, to test that it does the right things.