Although the World Tree had been subdued by Garon the Great Wizard, he did not clear the remaining World Tree Subbodies, instead letting them take root in the Green Forest World.
This was not because Garon the Great Wizard was particularly kind-hearted, but rather because he simply didn't bother dealing with these minor characters.
Moreover, as the barrier between the inner and outer worlds was broken, the spatial structure of both worlds was altered, and spatial turbulence and Elemental Storms would occasionally enter through Space Rifts into both worlds.
Though these World Tree Subbodies were not as capable as the main body, they could also absorb a portion of the disasters as nutrients.
With their presence, the damage caused by these storms was considerably reduced, which was beneficial for the world's recovery.
However, Garon the Great Wizard did not prohibit Wizards from hunting World Tree Subbodies—he just set a limit.