My take on it is that you need to mentally gear yourself to decide if you're going to have a JAMMA cabinet that also runs MAME, or a MAME cabinet that also runs JAMMA. And then, plan accordingly.
If it's a JAMMA cabinet that also runs MAME, then the ArcadeVGA video card in your PC and the J-PAC interface is the way to go. This combo assumes that you're using an arcade monitor (versus a PC monitor or a TV) and that you already have your controls wired JAMMA-style.
If it's a MAME cabinet that also runs JAMMA (which is what my next cab will be), you can just use a normal JAMMA harness, and make sure that you have disconnects in the wiring (like molex or D-SUB connectors) so that you can switch the controls to be wired either to the PC keyboard encorder or to the JAMMA PCBs.
But either way, it's definitely do-able.
(Edited because speeling is fun.)