It also appears always on the bottom left while other components appear right of the selected one.

I'm using AutomatedRedstone-1.12.2-6.0.4.jar with CD4017BE_lib-1.12.2-6.0.7.jar and InductiveLogistics-1.12.2-1.1.0.jar on Forge 1.12.2-14.23.1.2559

Output components are special in the way that they have no signal result that could be used as input for other components (they emit their result as redstone signal to the outside world instead) so they have a special reserved area on the board (the smaller one at the bottom). They are not allowed in the normal area also are normal components not allowed in the output area. Trying to move a component outside of its valid area will delete it. Also components gets deleted when pushed outside of the area by moving other components before it. This is how the GUI is currently intended to behave.

However I might decide change it so that the component move or insertion operations are blocked instead of deleting components.

Ahh ok - what got me confused was that the connections between others and the deleted output were rendering to go beyond the bottom right - and I thought I had somehow moved the thing where I can't get it back from :)

It might be a good idea to add a border to the output section, so it's more clear it's seperate.