Then the attacking monster would enter Tokyo Bay unless both spots are yielded and attacker enters Tokyo City? This is important because when monsters are eliminated and there become fewer than 5 players, the rules state that the monster in Tokyo Bay vacates their position leaving only Tokyo City occupied, so the exact location of a monster in Tokyo becomes relevant at that point.
The rules state
After a Monster that is not in Tokyo attacks, it must take control of Tokyo if either Tokyo City or Tokyo Bay are unoccupied or abandoned. If there is a choice, Tokyo City must be occupied first.
If Tokyo Bay monster doesn't take over, then there could be a scenario where the monster in Tokyo City dies because of a card leaving only 4 players and the monster in Tokyo Bay would be forced to leave, leaving Tokyo unoccupied.
Again quoting the rules
If a Monster is eliminated and that brings the number of Monsters below 5, Tokyo Bay can't be occu pied anymore. The Monster in it must leave Tokyo.
It seems to make more sense that Tokyo Bay monster would move to Tokyo City, but it is not spelled out.