The rules are necessarily set up like this in order to prevent fighters from exploiting the system to strip their opponents of a chance at winning the belt.
Let's say a vacant belt is no longer on the line if EITHER party misses weight. This means one fighter can cock block his opponent from fighting for the belt just by deliberately missing weight, which is simply unacceptable. In fact, if the reigning champion misses weight, the rule in boxing is that he is forced to vacate the title, and as long as the challenger makes weight, he can still contend for the belt. WEC didn't enforce this rule and Chael got screwed over in the rematch against Paulo Filho. Chael won, but since then MW champion Filho missed weight, the bout was considered a non-title fight, and Chael never got the belt.