Go to starsector/mods/nexerelin/exerelin_config.json. Edit the file with notepad or notepad++.
Look for the bolded line here.
Spoiler
"factionRuler": false, # gain same powers over a normal faction as you'd have with followers (probably not fully functional)
"corvusModeLandmarks": false, # adds some decorative landmarks in non-random Sector (will always be present in random Sector)
"useEnhancedStartRelations": true, # nicer starting relations between factions in non-random sector; e.g. League and Diktat are now only welcoming instead of cooperative
"useEnhancedCoreWorlds": true, # increases defenses and/or economic capacity of some core worlds in non-random sector
"useEnhancedAdmins": true, # gives named NPC admins some special skills
"useCustomBattleCreationPlugin": true, # affects things like map size and number of objectives
"officerDeaths": false, # officer permadeath (may be buggy)
"officerDaredevilBonus": false, # 50% experience bonus for officers in a frigate, 25% in a destroyer
"stabilizePackageEffect": 2,
"rebellionMult": 1, # higher mult means unrest will boil over into rebellion more quickly
"maxNPCNewColonySize": 6, # for new colonies created by colony expedition event
"hardModeColonyGrowthMult": 0.75,
"hardModeColonyIncomeMult": 0.9,
"colonyExpeditionInterval": 270, # days, starts in cycle 207; also note nex_expeditionDelayPerExistingColony in settings.json
"colonyExpeditionsOnlyAfterPlayerColony": false,
"enablePunitiveExpeditions": true, # if false, vs. competitor and free port expeditions will not happen (territorial ones still will)
"autoResistAIInspections": true, # default to resisting Hegemony AI inspections
"updateMarketDescOnCapture": true, # change market descriptions to reflect new controlling factions (only affects some markets, in non-random sector)
Change false in the bolded section to true and when you next start a game, it should prohibit AI from making colonies until you do. To find this line, you can open exerelin_config.json, hit ctrl + F, and enter something like "AfterPlayerColony", and you will search for that line.
However, if you have Lunalib installed, this will not work, as the Lunalib editor saves its own configurations. You will need to click the lunalib configuration tool at the top left of the main menu after starting the game and edit the options from there.