OK, this seems to work:
1. Start the game through the multiplayer/LAN menu, with just yourself plus AIs.
2. Play as normal till you spawn the colony.
3. Save the game.
4. Exit to the multiplayer menu and load that saved game.
5. Choose to play as the colony civ instead of the original one (this may require the "take over AI" option to be checked when starting the game, not sure).
6. When it says "we are waiting for cjb64 to connect", vote to continue without that player (your old civ will be taken over by an AI).
7. Proceed.
GP points apear to be retained OK. I don't know what other implications there might be from starting it through the multiplayer menu though.
On reflection this might even be an entertaining way of spicing up a normal game - I'm going to try it
Edit: Best to change the leader name, either of the old civ before saving, or the new one after reload, otherwise there are two "cjb64"s in the game, which is confusing! Just pull up the main menu and "Your Details" during play.