UPD:
If using Octopus and doing an "open jaw" in HK, you will be charged the average fare:
Airport>Hong Kong <>Kowloon>Airport (or vv): (110+100)/2=105
Airport>Tsing Yi<> Kowloon> Airport (or vv): (65+100)/2=82,5
Airport>Tsing Yi<> Hong Kong>Airport (or vv): (65+110)/2=87,5
If you are using a paper ticket, you would have to buy the ticket to/from the most expensive station out of the two.