1 and 2 are intentional. You're overlooking the fact that Settler's Colonies have a cost in both finite resource (colonists) and money. And by destroying them, you've not only wasted that investment, but lost a recruitment source as well. So all you're doing is trading one type of recruitment for another.
3. Someone trying to bring control to an unsettled region settles ex-soldiers - that's the whole point of colonisation. Even if it's just patrolling forts to guard the roads between whatever settlements are present in the region. Also note desertification of the Sahara hadn't progressed as far north as it is today.
You can't limit government types by specific settlements, the requirements work the other way around. Carthage's system is deliberately designed so that if you invest your colonists in a place, setting up the necessary infrastructure, you can build your governments. That's also why they can't build factional governments anywhere that doesn't have settlers present. Its part of what makes them distinct and different from a Hellenistic faction, for example.