Edit: Came to report a new issue with Alien Biomes, but for whatever reason, decided to hijack this thread...
From what I've noticed.... it seems that when Alien Biomes is enabled, stumps are no longer left after chopping a tree.
I was thinking it was the treeees mod, but I finally just tested with no other mods. Stumps work fine with only Terraforming enabled, but when I enable Alien Biomes, I'm not seeing the stumps being left.