I have an XDm 9mm Compact, very similar to your 40SW. Mine came with two mags, one flush, one extended. The extended magazine had the number 2 (medium) sleeve on it. They also ship a number 1 (small) sleeve and a number 3 (large) sleeve. They go along with the replaceable backstraps of corresponding size.
The extra magazine is a special offer that Springfield sometimes runs. I don't know if they're running one right now (probably not). But they may have shipped some during a recent special to LGS who had someone not pick theirs up. On the shelf it goes. When you buy it, they retrieve the case it came in, complete with your extra magazine.
By the way, you might want to try out one of the other backstraps (and sleeves) to see if either fits you better. I use the number 1 (small) backstrap and it made an amazing difference. I was a new shooter when I got the 9mm. My groups at 10 yards were in the 4-6" diameter range. When I changed backstraps, that dropped to 3-5". Still not great, but it was immediate.