The more I watch these streams, the more I notice. In the atmosphere logic, where he adjusts the sun, each of the sliders has an input and an output. This means there must be timers to interact with each thing (as well as logic of course) and each of the sliders must have a 'state' = to 'a set condition within the slider' that activates once the condition is met. I also saw a dark cloud icon which I'm assuming is weather. Taking what I've said above, the condition could them be 'when it starts to rain > raining for (set time) then = create puddles (logic set to animation).'
I've also been thinking about the easy animation and record function. Clearly, just as LBP, logic is going to eat that thermo up, so I can see a good solution there. Create your complex logic to make something move in a complex way, record it moving and then delete the logic. Thermo saved!