although you are correct that with a thermostat we want to regulate the temperature of the hardware (cylinder and head), we are doing so by regulating a intermediate (the cooling fluid). there is a relationship between fluid temperature and hardware temperature, but that is a very complicated one, depending on load, speed, coolant inlet and outlet temperature and maybe some other factors as well. and you still are not capable to directly regulate the temperatures you really want to know - the surface temperature of the head of the combustion chamber and the contact temperature between piston ring and cylinder. thus, the standard placement of the thermostat just outside the cylinder head has and had its drawbacks.
with the introduction of various emission regulations over the years getting the engine within its working temperature range as soon as possible after a cold start and keeping it within the optimal range as closely as possible a more refined regulating system is required. by controlling the inlet temperature keeping the amount of cooling within the optimal range becomes somewhat easier because you more or less stabilize the cylinder water inlet temperature depending on the load of the engine. in the classic system where you control the outlet temperature of the head you have less direct control over what happens because the inlet temperature will vary depending on speed, whether it rains or not etc with as a result the engine temperature will fluctuate more. you may also have noticed that regulating the cooling system has been increasingly sophisticated by the use of less fluid volume (leading to faster heating after a cold start) and more then one electrically driven multispeed fan effectively widening the range within regulating is possible. with "classic" system the range was managed by the thermostat only, in modern systems thermostat and fan(s) together do the job, making it possible for a faster reacting system capable over a wider range with less fluid.