From the
Modding Tutorial:
The facilities on the homeworld will be added as follows (all must be available with starting technology):
1) The Last facility with the Spaceport ability in the file.
2) The Last facility with the Space Yard ability in the file.
3) The Last facility with the Resupply ability in the file.
4) One facility that has the highest level of the Resource Generation - Organics ability.
5) One facility that has the highest level of the Resource Generation - Radioactives ability.
6) One facility that has the highest level of the Resource Generation - Minerals ability.
7) One facility that has the highest level of the Point Generation - Research ability.
8) Repeat 6 & 7 until the planet is filled.
Position in the file is irrelevant for the resource/research facilities. Technically, the Mineral facilites are added before the Organics and Radioactives ones (at least the first one is). But, they are presented in this order for ease of reading. There is 0 difference for in-game effects (unless you mod the planet used as a homeworld to only have 4 facility slots, of course).