I think that covering the box with the fixture is so common a practice that it would be "allowed by tradition."
Putting a bushing in the opening, though, is something almost never done- yet it should!
One little detail I add whenI mount a fixture this way: I add a small hole to the side of the bushing. This alows me to make my first support of the fixture by running a screw into the box. Then I can line up the light, and sink additional anchors.
That gigantic hole, if properly bushed, is the requirement. Check out NEC 410.14B.
If you're in a pinch where you need a hole to access the box, and don't have any sort of bushings here's a trick I use:
Figure out where your box is gonna in relation to your fixture. Drill a hole in the fixture that marks the center of the box. Use tin-snips to cut an "X" in the in the fixture, the hole you drilled should be at the center of the "X". Then fold back each of the triangles formed by the "X", and press them flat with your kleins or a hand-seamer. It leaves you with a square opening in the fixture, and the rounded edges won't knick your wires.
-John
I carry heatshrink in the truck in case I need to make a bushing for some odd size punchout... slit the heatshrink down the center and bend backwards to slip into the punched out hole. works well with 3" and 4" holes like these..