That might be what the in universe explanation would be, but it is not in line with historical examples. Certainly the US has bases, built on land it usually leases, but it negotiates uses of ports for the most part in foreign nations. The military is only initially the entity that distributes aid and oversees development, but that is turned over to other organizations as the security needs diminish. Given that Bajor reached the level of development that allowed it to join the Federation as a member, there would be far less need to Starfleet to be directly involved in its affairs. It would only need to rent facilities on DS9. If they really needed dedicated port facilities, Starfleet should be looking to build its own station.