This is not inconsistent, in most of the countries the Easter Bunny send easter egg to children, so the bunny in overworld can have lost all his eggs in the tracks

. (Maybe young player prefer rabbits instead of eggs ? I don't know

)
I also like the idea of an evil fox (Firefox?) who kidnapped all bunnies and hide them everywhere;
or little bunnies were scared when they saw nolok's "space ship" (In the first cutscene of the game) so they escape, and run in all tracks
to hide themselves 
. This could be a good explanation. We can also make bunnies with different colors

.
Then the boss could be a fox who took advantage that all the rabbit were found by the player to kidnap them -> It could be a race with this fox on "Land of the rabbit" you've just unlock (in a way that the fox is always ahead?), the fox kart should have a cage with some bunnies models

insid. There is no weapon on the map but the "mother bunny" give you 30 easter egg you have to fire on the cage to breat it the until 3 laps. The "cage life" could be indicated by a simple green/red bar above the kart like in "follow the leader" mode (it breaks with 20 eggs for example).
-> you can fire the easter eggs like cakes except they just go straight ahead

-> You win the fox character ?
Alternative with easter egg instead of bunnies:The final boss is exactely the same, there is one difference: Rabbit's mother tell you something like "The fox is catching my children! Use the easter eggs you find to defeat him! My sons are more important than chocolate

!"