I think a lot of the confusion arises simply out of the name "Flat Base" and the fact that we use terminology such as "base coat", "colour coat", "top coat", "clear coat" etc. People read "Flat Base" on the label and assume that it's used in a similar way to a "base coat".
I think the problem lies in the packaging, where X-21 sits in the rack right in the middle of a whole range of similar looking bottles. Package it in something that looks nearly identical to something else and people will try to use it the same way. It would have been preferable to have this item separate from the "normal" paint line with its own separate instructions for use.
However Tamiya are not alone in this. Gunze make a similar product and it is also "in the rack" alongside the regular paints. (Again with no particular special instructions) Next time you pick up a spray pack of Testors primer, see if there is any difference between the instructions on the label and the instructions on the label of a "normal" colour paint.