What are your theories about it?
That secretly, its Hasbro's discarded garbage
Or just some ancient magical artifacts created by some ancient pony race who's origin and existence has been lost through time but had some sort of future telling powers which told them to create these things to ensure the survival of their descendants thousands of years into the future.
Well a lot of the lore is inspired by Greek mythology, what if the tree came from an Apollo and Daphne type event?
I have a theory.
It might sound completely preposterous but here it is.
I think each of the branches... represents each of the mane 6.
My personal theory is that the Tree of Harmony is a World Tree.
Only, like, a different type of World Tree as it is short and crystal, instead of wood and just about beyond actual scale.
Its the physical manifestation of the origin point of Harmony in their realm. Harmony itself might have once taken root and spread through a system running all throughout Equestria.
Its why the box spawned from it (and the playset that followed) brought the Cutie Map into play - to further instruct the bearers of its fruit to spread Harmony where it no longer could reach.