The documentation should describe all of the built-in apps, hub interface, etc. Being a general-purpose automation system, there are so many possible things you can do with Hubitat that it would be impossible to have a document describing every possible automation any user could possibly want to create (though there are still many examples of such things, and even more if you look here in the forums).
Not quite. Do you want all thermostats to do the exact same thing according to the same sensors? If so, RM (and most apps) let you select multiple devices at once and send the same commands, etc. to them. If you want something slightly different for each but the same general pattern, the idea above of writing once and then cloning (and swapping devices) should work. If you want to try consolidating more devices into one "rule," something like webCoRE may be the best option.
You can share hub variables across multiple Rule Machine rules, eliminating concerns you may have about changing certain values individually in multiple rules. WebCoRE can use hub variables, too. This may help, depending on whether your concern is about values you may want to change across multiple rules or about the flow/logic of your actions themselves.
This is another reason I was not sure about your setup. 
You could use a virtual thermostat device that controls your "real" device (presumably some kind of switch/relay?), combined with Thermostat Scheduler (for time and presence) plus Thermostat Controller (to combine your sensors, unless there is only one per device, where you could simplify this layer a bit). Or you could look at custom apps someone may have already written for this purpose, maybe [RELEASE] Advanced vThermostat - Virtual Thermostat HVAC control. You can probably find more with a search.
Or maybe others who have created similar automations can chime in.
A side note:
The built-in integration works fine for many people; there were a couple features I wanted that were not available with it, so I wrote CoCoHue to fill those gaps for me and shared it here so anyone could do the same. Providing the ability to use custom code is an important part of Hubitat for me.
