In the example:
Il faut qu'ils aient leur permis de conduire.
They must get their driving licence.
Avoir us used here similarly to "avoir un exam". Here it means they must 'obtain' their driver's license.
But how would you say: "They must have their driver's license (with them)"?
Context might be one way, but if 'they' was ambiguous, the imperative sentence would be ambiguous.