ability:4 "AbilityBuildAlienShip"
I thought as much, but just wanted confirmation.
You'll probably need to set propertyType to AbilityDLevel in the entity files for the ability and the upgrade.
If you look at the other abilities & upgrades you'll probably find they have their own unique values of propertyType.
upgrade entity:
upgradeProperty
propertyType "AbilityDLevel"
value 1.000000
ability entity:
levelSourceType "StarBaseUpgradeLevel"
sourcePropertyType "AbilityDLevel"
just one other bit of info, starbases can only have FOUR active abilities
Probably explains why I haven't seen AbilityELevel yet

If all of those abilities are active then there may be too many.