Upregulation wouldn't explain why withdrawal symptoms decrease immediately.
I think you answered your own question -- the explanation you are repeating doesn't make any sense. In order for flumazenil to work through upregulation, it would have to reduce GABA-A signaling, which would produce withdrawal. On the other hand, the idea of it working through alpha6 is a reasonable proposal, because alpha6 is normally BZ-insensitive, so flumazenil (at the low doses used to relieve withdrawal) bypasses the receptors that BZ agonists target.
Action through alpha6 explains why flumazenil can be used in patients maintained on BZs -- if it was working through BZ receptors then to produce any noticeable effect it would have to displace the agonist that the patients were taking, which would induce noticeable withdrawal.