I can speak to the set up out of the box and the variax cable v regular:
I bought a used, non American JTV69 from GC to see if I liked it. Wow. Loved it right away. It didn't come with a battery so I had to buy that separately. Even the stock pickups sounded amazing to me. A little background for context, I started out my electric playing career on a Texas Special Strat - three single coils. Loved playing that for years. Then literally fell in live with the sound from a 59VOS Es335. Ouch, $4k. Then started getting a hankering for a Les Paul. There are so many models of LPs that I decided to go for a variax before getting into that.
K, now back to the used JTV59. I ordered a battery and it came without a charger, and buying the charger would bring my total cost up to really near the cost of a new one. So, I made the leap and bought a new JTV59 cherry burst. OML, the "Lester", strat and tele models are amazing. Have you ever dreamed of switching guitars mid-solo? I hadn't, but now I almost can't image not being able to.
The jtv59s come with fat, set necks, so probably not for you, but I wanted to answer your question about the condition of the guitar straight out of the box and the cable.
Out Of Box Set Up:
Set up was passable. Intonation was pretty spot on. Action was a little high, but they have to do that because the piezo will give you terrible thwaking from the low pitch strings if they buzz. I have worked it a bit to get it a little lower and I am somewhat happy with it. I'd like it to be lower. I. Going to work with a Luther to see about a b string buzz that, once removed, would allow for better action.
Variax Cable v 1/4"
I use HelixLT. So, JTV59 to Variax Cable to Helix. I can't tell the difference. There might be a difference, but I use the variax cable exclusively. I switched it to my Line 6 wireless and I couldn't hear the difference at low volumes. I didn't crank it though.
Lastly, I'm here looking at this forum because I'm wondering if there is a marked difference in the american made version. The reason I'm wondering is because this has become my #1. I really enjoy playing it and the versatility it provides. Iit isn't perfect,, but the sounds it produces are worth the trade off. Its a pretty high quality instrument, but I might be willing to pay the extra for a superb model.