Well, I do know that Klonopin is longer acting than Xanax, and doctors will switch patients to Klonopin in attempts to slowly taper someone off benzos.
I don't know about either working on different sectors in the brain; benzodiazepines all pretty much work the same way, or at least that's what I've gleaned from my readings.
In my early benzo career, I found the quick onset of Xanax beneficial, but its short half life meant I was dosing frequently. Many doctors shy away from Xanax because the quick onset is a prelude to addiction. My switch to Klonopin didn't do a thing for my addiction, and eventually my dosage was increased to horse tranquilizer level.
Benzos became the bane of my life, and I am duty bound to point out that it is recommended that any benzo only be taken for a short time, like two to four weeks, because they are very addictive and create a withdrawal syndrome that can be hellish. It was for me. That said, I question the veracity of any doctor that would prescribe a benzo long term. Since I've been in recovery, I have seen doctors that swear they never prescribed benzos because of the problems associated with them.