I connected a wire from a tweaked hub to an encased cogwheel that is only responsive on one side, but failed to respond to any input. I am unsure if the normal hub does this too, but it didn't work if I changed the input. I've been trying to make a 1 wide transmission with the tweaked hub, and so far this is the only issue, using Fiz2zy's tiny tank tutorial as a base. So far, I modified it to be free play legal, but it seems it necessitates links instead.

I don't understand what you are trying to say, tweaked controllers (like linked controllers) only activate redstone components via redstone links. If you are using the mod "drive by wire" then this is probably an issue with this mod instead.