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).'
Can't you animate it directly in that case?
I always found it fun to optimize my logic and watch it all in action behind the scenes. Boss with different stages was fun to make with blocks, sensors and wheels, yet my art is so crap it was more satisfying to see the machinery work instead of the moving lump of poo :)