Some of it is the inherrent snobbery of the guitar world. There's a pecking order where USA made guitars are the most expensive, then Japanese, then Korean, then Chinese (with the others somewhere in the middle). The quality scale matches the cost scale for the most part.

That said, the body will be made out of more pieces of cheaper wood - maybe cedro instead of alder. If it has a figured top, it will be a thin veneer of maple rather than a big chunk which will effect the tone (but you might prefer!). They will use cheaper pickups which won't have the same tonal response. They will probably use an 'own brand' bridge rather than a proper floyd rose or whatever.

Getting a guitar painted professionally would cost about £250 here in the UK, which would be about $500 I guess - you might get it cheaper but the long and short of my advice there would be not to bother buying a guitar you already know you don't like the finish on.

The USA guitar will kick the Japanese one's ass in all respects - if it didn't, Jackson couldn't sell it for 3 times the price, or whatever it is. The quality of finish / fretting / binding and all that sort of stuff is likely to be higher on the US made guitars...

Go play every guitar in your price range until you fall in love with one. Doesn't matter what it is or where it came from...