Then why not roleplay that the rebel inhabitants of Petra or Palmyra are not actually LOYAL SUBJECTS of the King of Saba. They are ALLIES of the King of Saba. Equivalent to the population of a city in your empire with a Type IV government - an independent city, but one that's very friendly towards you and pays you tribute.
A bit like early Rome. Rome didn't actually rule all of Italy directly in 270 BC. She just had lots of Italian allies, which had agreed to provide Rome with soldiers in wartime and allow Rome to direct their foreign policy (they still managed their own internal affairs). This can be simulated in EB by letting the AI automanage the 'allied' settlements while you control their armies.
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