Hmmmm.....
After the years, some of this stuff gets a little fuzzy for me but I definitely would expect to see a standard rounded-rectangle neckplate with a "Made in Japan" stamp on it, as you mentioned. However, the 3-screw TRC is typical of the MIJ bolt-ons (I just checked some old photos of bolt-ons I've owned and sold and they did indeed have 3-screw TRCs).
I swear I've seen an ED with that neckplate before... however, for all I know (and I would not be surprised in the slightest), this is the same guitar that's come up for sale again after several years.
In the end, my advice is usually the same - if it feels good, plays well, and you get a great deal on it... probably worth a shot.
No idea on the seller's assertions about serial numbering - that's the first I've heard of it and perhaps the seller knows something I don't (after gleaning all the information I can on the brand for almost ten years)

Although, honestly I've never given much of a damn about serial numbering since no info has ever survived to make it a viable ID'ing tool. He may have known a guitar shop owner or someone who passed that notion on to him. Another mystery.