The script can only see when a faction conquers a settlement. If they take it by waiting out the enemy or if it is gained through bribing or diplomacy, the script will not know this and no governments will be placed. If there is no governement, eventually the AI will build a government on their own, but it will usually be a Type3, no matter where it is. And yes, those spamming of levies is really annoying, hopefully the next fix will do away with both the palace recruitment and rebelling city CTD.