"(i.e. the second click will pass Insect Swarm because it is on cooldown) will it just pass clicking the button altogether and do nothing to the castsequence for the first button or will it increment the castsequence on InsectSwarm?"


The click macro does not consider whether the action is on cool down or not.
What is happening is when a comma is encountered its considered a valid command although it does nothing. This means that it can continue without "hanging" onto that part of the sequence.

The /click command press's the desired buttons in order it encounters them, and if an error, cool down or action happens it stops at that point. So when spamming this button your are simply hitting the key for one of those scenarios to happen. In your example its more accurate to say "the first click will cast Insect Swarm, the second will pass the comma in button1 AND continue to button 2 initiating moonfire".

The spacing of the macro and timing is based on many things, consider not every skill has gcd, mixed teams, cast channeling , HASTE etc. You as a multiboxer control all these variables, configure it in a way that fits your team.