You're right. At first, I thought this as a level design. It is not weird that some doodad acts as an obstable in games.
But after Tolbrynd, this becomes something different.
Rocks are uniformly considered as indestructible objects at Ipsilon and Tolbrynd.
But the large tree is not so uniform. It is indestructible in Ipsilon, but it isn't in Tolbrynd.
This is breaking consistency of this game and this may be considered a bug.
Especially when there's no explains about this in the game.
Maybe the trees in Ipsilon are tree-colored stones. Or maybe they used magic to strengthen the trees or something. Or maybe the trees on the other island grew up separately from the other ones, and didn't get the steady roots.
Maybe that's why Ipsilon is the first island, they're just a weaker country due to not being able to harvest their large trees.