Looks like it's because the equipment box does not change it's faction when the base is captured (it still belongs to FIA and offers FIA equipment, in the video when you hover over the map, you can see it's called Map (FIA)), so it's like giving the intel to the enemy's arsenal: no points scored.
There are many of these boxes that don't change faction affiliation, and some of the least noticable are the boxes with repair wrenches and fuel, because these items are no different between teams, but you still won't score points if you give intel to a vehicle depot built by the enemy, even if you control the base.