Frankly, you don't HAVE to take those Charisma perks, and considering they wasted like three perks for basically the same thing (point at X, make X do your bidding), I have little problem skipping all of them since that mechanic ---- threatening with guns ---- doesn't strike me as particularly charismatic.
I would suspect though, that it does not work in VATS. When you entered VATS in the old Fallout games, time would freeze and you could pick your targets (or not) and then you could "release" VATS time-stop and time would flow normally. With this new time-slow VATS, I am not sure if time remains slowed until you "release" it, or if action points burn WHILE VATS is slowing time, not just when you execute attacks in VATS.
I would imagine that to use the Charisma intimidation perks you have to point at a foe and ~not~ shoot them (obviously) and somehow trigger this Intimidation ability. Not sure how THAT will work --- previous Fallout did not have "hotbar" abilities that you could activate. If they have a dedicated melee button, and a dedicated Fire button and a dedicated Aim button, perhaps they have other "dedicated" buttons that you can press to activate abilities. Or perhaps just aiming at a foe (if you have Intimidation) will pop up context-sensitive button-prompts.
I fear, though, that you will have to put your cursor on the foe and hold it there at least long enough to trigger the Intimidation effect. Which can be hard if the foe is running around and darting behind cover, etc. Not a fan of this new trick, me.