AFAIK, as long as the two MacBook Airs have different names (i.e. John's Macbook Air and Mary's MacBook Air) there should be no confusion, and two independent sparse bundle files would be created. If the two are named the same, there might be confusion.
Also, you know it is pretty straight forward to replace the HDD in the Time Capsule with a new one. You might need a hair dryer to help release the adhesive on the bottom pad, but all else is easy to do. The end result would be more likely used than swapping a portable HDD around.