There are multiple views on this topic. Personally, I like the system mods better, and no, not because I install them

I think it's better because they directly connect to your neo, not an external box.
People have the stereo done at the same time so that they can use standard SVID and Stereo cables and not have to mess with the headphone adapter, or not use the MONO output from the A/V jack.
I would not recommend using the jacks on the Phantom 1 -- first, you'll have cables in the way, plus, if the cables get tugged, you'll put an unnecessary strain on the cart slots. Plus, they don't work on all model neo boards. Only the first gen board had audio lines in the cart port -- newer boards require a mod to make this work (running a couple wires).
Jeff