By the time you build a ecumenopolis, you would already have access to fusion or have a dyson swarm going on so that the energy needs can be satisfied, so whether or not you could build cities in or on the sea at the beginning of the society stage wouldn’t matter. The most analogous thing to an amphibious civ would be the Nile delta, you have water and it is flat terrain so you can farm anywhere, but as you build cities the area for farmland decreases, unless you farm on the roofs, but the population is still capped because the metabolism rate of heterotrophs is way higher than plants.
But if we discarded farming in favor of using solar panels with an efficiency 20 times more than photosynthesis, we could already fill the planet with a human for every 0.25 square meters. All we need to do is become robots. But verticalization of cities would still probably happen because it is more efficient if people who have jobs that are intertwined logisticly live close to each other. And you can go the other extreme. There can be a single hive city in the planet. And a natural disaster can take it out all at once.