Why not? I haven't been on a factory tour, but I did watch the NatGeo (? Perhaps a different channel...) episode and I worked for a summer at a BMW plant (although over 20 years ago).
Modern lines are virtual lines, not physical. The unibody sits on a robot that moves from station to station. Assembly happens at each station... Since the X and S sit on the same platform, all the hard points will be identical. Installation of things like the dash will be 95% the same -- only bolt locations will differ (and both robots and humans can handle those subtle differences). The biggest difference will be installing the rear doors, no sunroof for the X, etc. They may have to set up a couple model-specific stations to handle those...
When I worked at BMW, I built 6-cylinder engines on a physical line. The next line over was for the V8 -- and was a virtual line. It took less than half the space to build a more complex engine. I wouldn't be surprised if BMW now builds both engines on the same virtual line and just trains the assemblers on the differences. Even when I worked on the I-6, I could visually identify the variants -- there were subtle differences for ones that went in the 3 series from those that went in the 5 series, and they took different parts (different length dipstick for example)... In fact my visual ID was faster than waiting for the monitor to tell me -- so I just used the monitor as a verification step at the end...