They don't recommend anything, in fact it seems like they go out of their way to make it clear it can run both ways, up to "rider preference." I suspect there's a liability risk for them telling you a better way to set it up or something.
When the brake was on top, it slams into the master cylinder/exhaust valve lever thingy and sits up really high, even using the mirror as a spacer the two levers are almost 90° from each other. So I tried rotating them to split that difference, but that just made using both levers really uncomfortable- having to reach way down to shift, and still having to twist my wrist back to grab the brake. It was kinda cool being able to raise my index finger to pull the brake down, leaving most of my hand on the grip, but I'm not sure how practical that is anywhere but on the stand in the garage.
Flipping it around so the brake is on bottom gets them as close as possible, about 45° apart. At least now I can grab either lever while leaving my wrist and hand in more or less the same position. I didn't even notice the brake while riding this morning, was still able to use the clutch naturally.
There's less protection of the lever with it down low like that, but yeah I think the bark buster should still protect my hand in most cases. I guess I could see a major front end impact where an object goes right through the hand guard, then presses the clutch into my hand, but geez it's a motorcycle that kind of vulnerability is everywhere. Plus my instinct is likely to pull the clutch in. I'm not ready to lose the clutch yet..