As a bonus you can then buy old PCBs and switch between either your Pi or a real PCB.
It's also much simpler: no need for complicated controllers and whatnots for all the heavy lifting is done by the Pi2JAMMA adapter.
It's what I have: a real arcade cab (a vintage one, from the 80s) but "modernized" in that at any time I can switch between real PCBs (I've got both real vintage PCBs and vintage bootleg PCBs: a prized possession) and my Pi+Pi2JAMMA.
I take it anything that can be run in TFA can be run on a Pi: I'm not sure if that project does something that couldn't run from a Pi with a Pi2JAMMA adapter so maybe I'm misunderstanding the (cool and good looking) project.
The marquee that's a display that can change is nice: I've seen a few arcade cabs (on arcade cabs forums) that had these and they'd switch the picture depending on the game being played.