I don't think mine are similar to yours. What make are they? I can't visualize how the short bolt thing would work unless a different valve cover bolt is provided with a threaded head to accept the short bolt.
I just noticed that the rear aperture of the protector is better aligned, so I'll test your theory tomorrow, but from looking at my other protector-less RT, the bolts look the same height above the mating surface of the valve covers, and I should think that they'd have to be long enough and torqued down enough to withstand a crash. I had a brief moment of epiphany when I thought I'd just remove the accessible rear bolt, then rotate the entire unit around the front bolt and out of the way of the front bolt. Then I realized that torquing it down would probably make rotating back into place impossible. Damned if you do . . . Thanks for the input, and I'll let you know.