I suspect that's a bit of marketing blurb.
Yes, they probably do 'build them from scratch' as a distinct catalog item - but only in as far as someone says "Right, shunt this lot down to the plating department."
And yeah, it makes no sense at all to fully assemble a horn and say "Oooh, this one's nice" - then rip it apart and plate it.
Commercial suicide, in fact, given that there's barely £200 between one and the price of a lacquered model.
The way I interpreted that language, basically the same as the way you interpreted it:
The clear lacquer one is the YTS-62
The silver plate one is the YTS-62S
there are other ones
So the factory gets an order from the MRP system ("materials resource planning") that says this week you're going to make 35X 62 tenors, 7X 62S tenors, 480X 52 tenors, 800X 25 tenors. The 62 and 62S tenors have identical processes up to the point of finishing; but at that point after leaving the polishing process, the 62S parts go to the plating room and the 62 parts go to the spray booth.
Of course at this point they aren't saxophones yet; they are bodies, necks, maybe the back side key guards are also separate, and a whole bunch of keys. For that matter, since Yamaha 62s have detachable bells, the bells may be separate parts at this point.
The bells and bodies come together, then the keys get assembled, then the last few other parts, and only then are they going to start putting necks on bodies and actually having something you could call a saxophone.
So, yes, the 7X silver plate 62 tenors scheduled to be built this week, are identified on their build tickets, or travelers, as "S" from the beginning; but that doesn't mean there's any difference in the parts used to build them until the plating tanks.