It's a bit dumb that colony capital placement is always random. Quite often I would prefer to be able to place it manually for the optimized tile usage.
I've just devised a quick simple mod as a crutch solution for the problem: you can now destroy your colony capital and rebuild it as any other improvement on any tile you wish with minimal production cost (will always take just 1 turn). Unfortunately mod won't work if you're loading old saves, but in a new game everything works like a charm.
How to install:
1. Download it
2. Unpack into your mod folder (My_Documents/My_Games/GalCiv3/Mods)
3. Make sure 'Enable mods' is checked in game's options menu
Current version has a bug that allows you to build surplus colony capitals on other planets once you destroy it somewhere, I'm looking into fixing it.
As the game gets updated, I will also keep track and update my 'mod' to the latest version.