I bought the bike in Chiang Mai, and it is exactly what you describe. It was brought in by a Bangkok importer who aquired it in Japan, took it apart, and imported it as a pile of parts. The parts were sent up to Chiang Mai and bolted together by my mechanic.
While the parts were legally imported, you are correct - a motorcycle was not. I believe that the import duties on parts are about 30%, while a bike would be 80% or 90%.
That is why you have to pay these high fees to get a plate. I paid 60,000 baht for my plate, and I know the fees can go higher. It takes a long time, and gets done at an office outside of Bangkok on the weekend. Mine took almost 1 year to get.
As I said, all I had at the time was a handwritten bill of sale from my mechanic - in English. The import papers for the parts existed, but were in Bangkok with the registration paperwork. The US plate was an expired one from my bike in the US. I had no US papers - the plate was decoration while I was waiting for the Thai plate. The police report just said that the bike had no plate.
But this is Thailand, and in Chiang Mai. There are countless big bikes for rent here, and 99% have no plates. No doubt that other areas of the country might do things differently.
I would not believe any rumors that bikes get confiscated, until I hear a first hand report. Anyone out there that has had a bike confiscated for lack of plate?
BobS