You're right about the 3/4 Basic Support difference. There's 3 BS in the GC2Ships.xml and 4 in the S0_ColonyShip.shipconfig. The extra Colony Module is just for show btw.
GC2Ships.xml:
<Ship Name="ColonyShip">
<DisplayName>Colony Ship</DisplayName>
<Model>ColonyShip</Model>
<Description>Taking people into that great big galaxy.</Description>
<Component>CargoHull0</Component>
<Component>BasicSupport</Component>
<Component>BasicSupport</Component>
<Component>BasicSupport</Component>
<Component>HyperDrive</Component>
<Component>ColonyModule</Component>
</Ship>
S0_ColonyShip.shipconfig (with all the positioning data deleted):
[HULL]
Version=26
BASE_HULL=S0_Cargo_0.x
Dummy01_Component=Structure156
Dummy01|Dummy01_Component=Structure312
Dummy01|Dummy01|Dummy16_Component=BasicSupport
Dummy01|Dummy02_Component=Structure19
Dummy01|Dummy02|Dummy01_Component=Structure200
Dummy01|Dummy02|Dummy04_Component=BasicSupport
Dummy01|Dummy02|Dummy13_Component=Structure200
Dummy01|Dummy02|Dummy24_Component=ColonyModule
Dummy01|Dummy02|Dummy25_Component=ColonyModule
Dummy01|Dummy02|Dummy36_Component=Structure312
Dummy02_Component=Structure2
Dummy05_Component=Structure2
Dummy14_Component=Structure2
Dummy15_Component=Structure2
P0_Component=HyperDrive
P12_Component=BasicSupport
P13_Component=BasicSupport
P21_Component=Sensors0
P22_Component=Structure156
P22|Dummy01_Component=Structure107