I personally am glad i have both. i debated ditching the factory tie down sliding hooks when i installed the molle since it ate up space on the molle panel but im so glad i put them back in. I love being able to slide the tie down hooks exactly where you need them. The molle panel have plenty of space anyways. I like both but depends on your use case. I use both regularyly and have so much stuff on the molle panel. i personally wouldn't ratchet strap anything to the molle panels as a tie down point.
Things i have on molle:
-tow strap
-hatchet/sledge
-dirt shovel
-snow shovel
-python cable lock
-saw
-dry bag
-dead blow hammer
i keep my kinetic rope and rigging in the cab. Id like to get the molle panel that goes against the front of the bed (against back window) then add some traction boards to it. Last im going to put a offroad jack mount in the bed, my buddy designs and makes the mounts for the badlands one that goes to the bed. just nervous to eat up that much space when i mainly haul dirtbikes and drill holes in bed..