Population is based on the level of the buildings an empire has. Every building gives 10k of populations per level. The only exceptions to this are glyph buildings including the Gas Giant Platforms, and the Terraforming Platform.
Colonies referred to as Bleeder colonies have sometimes been used to take the top colony position since deployed bleeders both upgrade automatically and do not take plots. However overcoming the unhappiness produced by the bleeders is a challenge it is theoretically possible to do it with a level 30 Junk Pyramid and Space Junk Park.