If I understand things correctly, the Biosphere Manipulator is supposed to be the Altarians version of the Ultra-Terraformer. The amount it takes to use one to fix a tile certain;y suggests that. As does the fact that the tech that unlocks it (Paradise Worlds) gives a separate improvement that allows one to upgrade any tile anywhere on the planet at the same time.
However throughout the beta, it's been a one per planet, unlike the Ultra-Terraformer. This puts the Altarian faction at a severe disadvantage to all other factions since with the Ultra-Terraformer, they can upgrade all low level tiles on their planets while the Altarians cannot.
In fact, if I read things right, being able to get their version of the Ultra-Terraformer "early" (in the Age of War as opposed to the Age of Ascension) is supposed to be a perk for the Altarians. But as it is currently implemented, it actually hurts them as they can never "catch up" to the rest of the factions when it comes to upgrading their worlds.