Note that the colony cost during generation is for the default (SM) race, NOT the race that you'll end up having. When you pick a homeworld and generate your race, the race's tolerances for gravity, temperature, oxygen etc. will be set to make the homeworld "perfect", i.e. the colony cost will automatically be zero, even if it was showing up as e.g. 1.6 before.
Duh! Thanks, that makes sense now.