Yes. There may be complications when you try to equip items on the sovereign from the sovereign creation screen.
The information for custom sovereigns is gathered from each racetype (CoreRaceTypes.xml) where male and female sovereign types are defined. Ex:
<MaleUnitType>Generic_Sovereign_Altarian_Male</MaleUnitType>
<FemaleUnitType>Generic_Sovereign_Altarian_Female</FemaleUnitType>
those unittypes can, of course, be found in CoreUnits.xml
