Normal Empires get a Merchant job every 50 Pops, and it at least adds 8 Trade Values, and therefore minimum 4 Energy.
But for Hives and Machines, we get a Coordinator or a Synapse Drone every 20 Pops. These jobs produce Society and Unity, and each has an upkeep of 3 Energy. So instead of making more Energy, we just suddenly earn much less by completing the tree.
You'd think the Prosperity Tree is something you want to do when you want a more stable Economy, not because you want to add +3 Unity and +3 Society each planet.
But for Hives and Machines, we get a Coordinator or a Synapse Drone every 20 Pops. These jobs produce Society and Unity, and each has an upkeep of 3 Energy. So instead of making more Energy, we just suddenly earn much less by completing the tree.
You'd think the Prosperity Tree is something you want to do when you want a more stable Economy, not because you want to add +3 Unity and +3 Society each planet.