So I cannot say for sure what SA has done, I will say the site looks like they are moving in the proper direction of offering 10mm and .45ACP in the XDm. If they did offer it in a .40 before, which I believe they did, they realize that the .40 is being phased out. The FBI stopped using them a few years ago. Honestly I wouldn't pay attention to what military and federal agencies carry anyway.
Right now the focus is primarily on 9mm. For those of us who own and prefer larger calibers we are either set in our ways and prefer the .45ACP, have explored the versatility of the 10mm and are sold, or have likely added both to the collection. Read up on the 10mm if you are looking for a larger caliber. I would not go with .40S&W.
More importantly try them all out.
What extras do you think should be in a SA case? Magazines? As far as I know they have run promotional offers like most but standard for out of box extras can include up to three magazines, speed loader, chamber flag, and a cool guy sticker. Any more and I would say it is promotional.