Hi Tony,
I did see that thread at the time, but decided not to comment. You didn't say how you came by the set, or whether it was in its original wrapping. In other words the question that comes to mind is "Do you have anything that indicates the two stoppers came with the decanter/set originally?"
If not there are a number of ways that two stoppers could have ended up with the set you bought, the one that comes to mind first is that a second decanter was broken. It could have been lost in a move by the previous owners, etc, etc..
As for the different thicknesses, this could be down to the individual workers, or the different times it was made. In all likelihood it was different workers who took different amounts of metal (glass) on the gather, so producing different thicknesses. In my limited experience, the more experienced the blower, the less glass on the gather and the finer the finished item becomes (unless the item is required to be consistently thicker). Maybe Adam could comment on that side of things?
Without some sort of definative proof we are only guessing that the stopper was sold (or commonly used) as a glass. Of course, it is quite possible owners without the matching glasses could have taken the odd dram using the stopper

Usage might be different to the original intention of the designer or seller, but again that would be apocryphal.
Nigel