I think you should run your levers the same for all the bikes you own. If you run reverse on one bike, do it on all of them. If you're running it one way on your road bike, I'd run it the same way on your 'cross bike. I run all of my bikes with left to rear, right to front. This is mainly due to my regular motorcycle riding. I figure I don't want to be in a panic situation on any of my bikes (or motorcycles) and grab the wrong lever out of habit. True it helps with 'cross when you're coming to the barriers a little hot, but I think consistency is the more important factor.
I've never had a problem switching back and forth, but that's mainly b/c I stop racing road and start racing cross, then vice-versa. I ride the road bike during cross season, but braking order isn't as big of a deal in that case. Beyond that, I tend to prefer to brake with the front on the road bike and rear on the cross, so having the levers swapped actually makes it work out fine.
you should always run with the rear brake the same as being right or left handed. the reason being is that if you have an emergency you always use the hand that is your preference
if you are right handed and your front brake is on the right then if in a cross race it will cause the front end to lock up and you dont need this.
so if you are right handed the front is on the left and the rear on the right, if you are left handed the front is on the right and the rear on the left.
some people who ride motor bikes prefer to set up there bikes with the front brake on the right .
There is a good reason why the rear is on the left if you dismount on the left side. Try slowing down with the rear brake set up on the right. Maybe some of you can but not at speed. Or another approach is set it up what ever makes you happy and comfortable.
I run mine "backwards" - makes it easier to scrub speed if necessary before a dismount. I have my road and mountain bikes set up the same way - that way I don't have to think when switching back and forth between bikes.
I switched them last year. One of the best upgrades on my cross bike I've done. Definitely a huge advantage for scrubbing speed before barriers. Especially those ones on a downhill. I definitely improved my speed through barriers.
My road bike is setup traditional. The switch isn't too big of a deal. However, I only use my cross bike for racing, so I don't slam on my brakes to avoid crazy drivers on the road.