I would find a 2016 500X in a showroom and look for yourself.
And I also checked the Fiat UK website and they list the space saver as "standard".
This could be a typical Fiat UK website not keeping up with latest changes?
Also, changing the rear floor pan to have or not have a wheel well is an expensive production alteration.
IF the space save is no longer standard then this is what I think Fiat have done:
1) The wheel well still exists
2) Instead of the wheel the well now contains a plastic wheel insert that contains/holds the jack and tools etc. that were in a separate bag that stored to the side of the well and below the moveable elevated floor cover
3) The bracket that supported the false floor may have been removed
In my 500X (2015) I can remove the space saver and drop the false floor to the lower level. This gains around 8 to 10cm of boot depth.
I do not believe that Fiat would change chassis production for a few plastic bits.
With this in mind I think the "under slung" wheel is nothing but sales people not understanding what they are talking about. In any case unless Fiat have changed the exhaust system as well then the under slung wheel would be very difficult to access. Add to that the loss of rear ground clearance then I think that 1) 2) and 3) above are more than likely the difference between space saver and no space saver.