My understanding is that it's not uncommon for VA to bill insurance, and they theoretically attempt to bill whenever possible (and appropriate). I vaguely recall them mentioning this when discussing why providers shouldn't just automatically check that a visit is service-connected when it may not be. But considering most patients seeing MH providers in VA are service-connected for MH diagnoses, it may not come into play as much for psychologists. Anecdotally, in all my time at VA, I got exactly two emails about insurance that required additional information on my part (e.g., how long I spent administering each test), and the end result was that the insurance company said I could've billed for more. So I suspect MH providers are, more commonly, at the mercy of the billing folks at their own VA in terms of what actually needs to go into the notes. But to your point, no, I don't ever remember hearing of anyone at my VA needing to justify using the 53+ minute codes, either.
As for the LEAF system, at least at my VA, they were severely protective of access to the ability to setup clinic grids. At best, each service, or perhaps even each hospital and CBOC, had one person with those privileges. There are indeed specifications you can set as to how many overbooks (if any) can occur. We also had individual clerks assigned to groups of providers so they could better understand the ins and outs of each person's clinic (e.g., all new patients go here, all follow-ups go here). The part that was always especially aggravating for me was the inability to book into a specific clinic at all, even as an overbook, if you didn't have at least one normal (recurring) clinic slot on that day. So let's say I typically see my testing patients on Mo, Tu, Th, Fr, and I want to fit someone in on a Wednesday to get them in ASAP. Not gonna happen in that testing clinic. Same goes for feedback if I normally see those on Wednesdays but wanted to work someone in on a Friday. So that always required lots of finagling and instant messaging with clerks.