I think it had to do with the swap from no plug in the rear end housing to plug in the spec case when these mix in some cars came up with both. So maybe the spec case with the plug came earlier than the rear end with no plug.
Yes there was not attempt to coordinate the two changes other than to make sure at least one had a fill plug
An additional thought about the housing research. You should seek out and include Mustangs built at San Jose with 9" rearends since there was no different for workers for that item between Shelby and Mustangs and it will increase the pool of information a fair amount. Do currently, on record, have just less than a dozen examples of those with fill plugs on cars assembled/finished in the month of June 1967
Also if you want to go deeper for the third members a shadow survey of 9" third members from none and early 3rd members from other Fords would help add allot more information as to when the change at the producer of the third members switched from the no-fill plug to the fill plug version.
I've been doing both for a number of years but have not updated or focused on these two specific patterns lately. Hundreds of similar ongoing surveys. Some published on CMF