It is certainly implied that the sapling from 12,000 B.C. is the same as the sapling in 1000 A.D. but it is not explicitely stated. Given that you can't complete that side quest if the Lady in Zeal destorys the sappling, there is certainly a connection but the nature of that connection is unknown.
Certainly the magical powers of the sapling seems to be relevent to the discussion. It "saved the environment," Robo was able to use sap from trees in that forest to make the Green Dream, the forest is where we learn of the entity, Lucca's portal was there, and it may be (though there is no real evidence) that the Astral Amulet might contain a cutting from this forest/plant.
To note, however, referencing Placidchap's statement regarding deserts; deserts are fairly seldom devoid of life. Even Death Valley can be covered in flowers at times.