are you creating the starbase using a DistantStars type of npc starbase deployer or -in rebellion- just adding your starbase to the galaxyscenariodef file and putting it in the piratebase?
You might want to make some custom starbase upgrade items. This one is Entrenchment (not sure if different from Rebellion) and gives NPC Corpo StarBase block colonize. The moment the starbase is built, the upgrade is there. You can do the below for Toughness, Trade, and Hangar. You can give the starbase abilities like flakburst, telekineticpush, powersurge, repair cloud... or even make the starbase mobile (see end).
TXT
entityType "StarBaseUpgrade"
stageCount 1
stage
price
credits 0.000000
metal 0.000000
crystal 0.000000
upgradeTime 0.000000
nameStringID "IDS_STARBASEUPGRADETECHBLOCKCOLONIZE_NAME"
descStringID "IDS_STARBASEUPGRADETECHBLOCKCOLONIZE_DESC"
researchPrerequisites
NumResearchPrerequisites 0
hudIcon "HUDIconStarBaseUpgradeTechBlockColonize0"
smallHudIcon "HUDIconStarBaseUpgradeTechBlockColonize0"
infoCardIcon ""
upgradePropertyCount 2
upgradeProperty
propertyType "MaxAntiMatterPoints"
value 1000.000000
upgradeProperty
propertyType "AntiMatterRestoreRate"
value 5.000000
upgradeBoolPropertyCount 2
upgradeBoolProperty "CanPreventEnemyColonize"
upgradeBoolProperty "CanPreventPlanetLossByBombing"
Mobile Starbase
rotateFacingType "None"
rotateConstantly FALSE
maxAccelerationLinear 40.000000
maxAccelerationStrafe 4.000000
maxDecelerationLinear 500.000000
maxAccelerationAngular 0.500000
maxDecelerationAngular 9.999996
maxSpeedLinear 275.000000
maxRollRate 1.000000
maxRollAngle 15.000000