Since I don't have a 900 my answer may not satisfy your needs... But on my 05 Nomad the stock OEM bars do not touch down until AFTER the floor boards have scraped and flexed up. And the few times I've scraped my floor boards I was so startled that I quickly righted the bike so going far enough to touch the bars was not a consideration.
As you mentioned going over far enough to fully flex the boards up means you are close to lifting the tires off the ground and at that point you are screwed and probably would want the bars to be there since you are about to go down and would want the bar protection for your legs...
