So what's with items like the emergency afterburner requiring both a dedicated "on" and "off" key?

That effectively means you need two joystick buttons for one command.

Have the devs ever explained why that is?

If you have a programable joystick you can have a button that sends one command pressed the first time and a diferent command a when pressed again. Sounds like it may be what you are looking for.

It's for programmable joysticks where you want to ensure that the inputs remain synced.

If I'm programming the FlapsUp button on my Warthog throttle, I want to give it a "Flaps Up" command not a "Toggle Flaps" command. This is because I might have left the switch in the wrong position from a previous mission, in which case hitting my FlapsUp button would result in the flaps going down.

Having distinct actions defined makes programming the stick much, much easier.

Nothing preventing developer adding all commands: state A, state B, and toggle state. Then everyone can have the ideal control setup.

This

+1. While you can program discrete commands into an array (e.g. using SEQ in TARGET) and even create functions to keep track of them, you still run into minor syncing issues when you get shot down and have to jump into a new plane. Not to mention that some programmable sticks don't allow sequencing.

My vote is for both discrete and cycle/toggle iCommands.