The water might be safer if the xrays damage or kill bacteria present in the water or on the bottle. Water is unaffected by Xray radiation.

With respect to the materials, xrays don't modify metals. Xrays over time will change plastic polymers, but the amount, duration of exposure, and intensity are more than a medical xray. Multiple forms of radiation including UV light will modify or break polymer bonds plastic over time. This is why plastic tends to "bleach" in the sun and turn white and powdery as they degrade. Bury plastic underground and it will last a very very long time.

I can't see how an xray would do anything to a water bottle that would affect its safety.