Just something that the wiki might have made clearer.

Its hinted at that some of the gates have alternatives. Its not stated exactly what they are.

The alternatives are selected by using a screwdriver and right-clicking while crouching.

Normally the screwdriver just rotates the gate.

With the NOR gate you can select which inputs are active. I think there are seven options, all the combinations except "no input".

With the NOT gate you can select which outpus are active. This allows you to suppress unwanted outputs.

The RS latch is an odd one. There is a flipped version of the basic latch, then there are two versions with a different logic drawing. It took me a while to figure out they are a non "leaky" version of the latch. Normally the latch inputs are also outputs. With the alternate they are not.

The timer doesn't appear to have alternates, but crouching gives you the gui even if holding a screwdriver.

The state cell has a mirrored version.