You cant capture the mountains or sea vents, those messages appear in error when you click! The game was originally supposed to have the ruins of existing buildings all around the map that you could capture and repair, but I didnt have time to draw ruined versions of buildings for that - and I forgot to exclude mountains and sea vents from being considered "buildings" when you click on them. Whoops!

What the crane does is it expand your buildable area by many tiles, to make it easier to build large buildings, or to build some things away from your other structures.