Usually molex is run from 18awg cable, ~5a gives 60watts 12v and 25w 5v. Extra connectors reduce the load on each one, which reduces the heat. (The connector itself is rated for 13a, but no one wires it with the 14awg that would need). I haven't pinned any of these out, but I'd make a bet that the multiple plugs are just hooked up in parallel; and using different supplies would be a bad idea; due to possible different voltages.
CN: I'd use both, as it will make a fire less likely.
