I plugged in my controller just to test this and I don't know what you're talking about? Pressing the confirm button twice behaves exactly like numpad-0 on the keyboard does for me. I.e. If you don't have something targeted then it will autotarget the closest NPC/object and pressing it a second time interacts with it. Locking onto something requires pressing down on the left analog stick (L3) which is a completely different button press entirely. I'm using the default filter "ALL" and haven't made any changes to the default gamepad settings and have zero issues targeting and interacting with any NPCs in a mob of people using the confirm button twice.
Edit: also tested on a summoning bell in Limsa surrounded by a bunch of people while standing at a distance so they'd be in the way. Just pressed A twice (I'm using an XBOX controller) and accessed it.