Currently, it looks like if you wire up a circuit with "Set Filters" and multiple values on the circuit, the "first" two values >0 will be used for left and right side filters. What's the logic behind which is chosen, and which is applied to the left and right sides? I tried controlling with red and green but that doesn't make a difference, I tried changing values to see if higher/lower values would affect which is right and left, but that didn't make a difference either.

What is the intended functionality of the "Set Filters" circuit network input?

The loader prototype sets the filter over the wires in alphabetical order. I can't change that, it's in the game.

I see. Well I guess we can't expect super polished behavior for something that's not "officially" part of the base game. Loaders are weird.