I imagine it isn't any worse on your bones than sitting on the couch eating nachos.
Keep in mind that the study was done on competitive racers who spend a LOT more time on the bike (and a lot LESS time doing other things) than most people. We've all heard the adage that when not riding, pros need to be sitting down to rest...unless it's possible to lie down, in which case they should do so.
If that's your lifestyle, it's not suprising that you'd have some odd health anomolies.
When you run, you stress your bones, and that generally causes them to strengthen themselves. At the same time, running is tough on your joints. Cycling is easy on your joints, but doesn't help with bone denisty.