In the context of the Israeli/Palestinian conflict:
Settlements - refers to illegal makeshift “towns” (usually no more than a few trailers) built on lands that belong to Palestinians by right wing Israeli extremists who believe that the entire land belongs to them. As of 2006, these are strictly in the west bank.
Everything else (city, town, kibutz etc) - traditional meaning but also indicates that they are within the official internationally recognised Israeli border.
Bolivia signed a large defence contract with Iran recently, so it really depends on how it unfolds.
If it becomes a way for Iran to establish an outpost in South America it may lead to political assassinations and a regime change.