Major differences include spoked rims and modern plastics on the XR to mimic the larger XR bikes. There may be a difference in the frame or suspension, not sure. Otherwise very similar. That engine hasn't changed much in nearly 40 years.
Check with Lyle at Classic Honda. Those guys do nothing but Honda minis, and they know their stuff. I'm pretty sure that the '93 & up Z50 has the same engine as the XR50. The biggest difference between my 71 Honda Mini and my 03 XR50 is the roller cam head on the XR. The 93 and later Z50's have the roller cam also.