Curiously, I have noticed lately that on the programs' websites they are noting that they will pay for the Step 3 exam. I'm guessing they are utilizing this as a "perk" of the program. They do give the two days off without penalty.
To your second point, more and more programs are leaning towards having the test past at some point in the residency, some opting for it to be done prior to the second year beginning, and some prior to graduation. From what I've seen, that seems to be the trend in the last few years.
Hope this is of some help to you. Good luck!
Nu