A question: If I wipe out Van Graffs, will somebody take over the store and sell energy weapons?

Nope. If you wipe out the Van Graffs, only Knight Torres at the BoS will still sell energy weapons.

Gloria sells some unique weapons like Cleansing Flame. Will Torres have the same array of inventory?

Looks like I'll have to do some dealings with console command before I start shooting

Their stock goes to the vendortron at the gun runners. Same happens whenever you kill any weapon shop. But there is a bug that doesn't update the robot's stuff. If that happens then take off GRA and then put it back on and see if that works.