All those Y bike numbers must have been chosen from the 1967 despatch books.
I am not convinced they were picked in any particular order also.
Given some of the info GaryE has provided, it appears that all of these "Y" bikes were replacing previous bikes that had been withdrawn from the market, for whatever reason. They must have been working off of a master list of these defunct 1967 bikes.
They probably continued to add numbers to this list as production went on, that would help explain the 4 digit numbers like MotoMikes showing up as late as December 1969.
The stamping guys on the engine assembly line would have been right up to speed as they would need to add in the low numbers under 10,000, and then work in the LA, TA, and RA "Y" numbers at the same time as they were producing the 1970 engines. I doubt very much that they were duplicating normal 1970 numbers, say A65LA12222Y and XD12222A65L, the engine stamper was probably stamping the A65LA, A65TA, A65RA on as well.
MotoMikes number suggests that the "Y" was left for the stamper on the final assembly line, that person would have needed the "Y" stamp for the frame anyway.
So, as you suggested, the guy probably used the "X" when he intended to use the "Y", then just added the "D" as that is the exact combination he would be using to date the very next bike down the line.
The numbers just seem all over the show.
We would need to see the 1967 and 1970 books to have a fighting chance of working that stuff out.
Yes, it would be a great help to have full on access to the 1967 through 1970 books. Some of these numbers hit three of the four years, with only slight variations!