Eminent Domain does appply because the planet was never the Baku's. Even Picard, a supporter of the Baku, acknowledges that the planet is in the Federation.
My house is in the United States. It doesn't make it the property of the Federal Government until they seize it. Because it moved over the course of 300 years to Federation hands, that's making my point for me. They have a longer claim on it than the Federation does. This is moving the Native Americans off their lands. They migrated from what is now Asia over Alaska into North America. They were indigenous to the region. Eminent Domain certainly does apply. They are not Federation citizens. They were not consulted about the future of this world, as the two examples you have stated, have been. Without Data going crazy, the Federation would've killed 600 people, asking them to "slowly die." Like the Ba'ku or not, that is what they were being forced to do.