It looks like the selection box of the ingredient renders in a different spot than the ingredient itself when padding is non-zero. I'm not sure if this was already fixed at some point or if this is an error on my part, but I do hope I'm not all stupid all of the time.

Looking up the documentation on JEI again, it seems this explicitly only refers to the rendering of the ingredient and not the hover-tooltip-stuff..
So.. for all this is concerned, it seems to do its job? It renders it slightly offset as you see in your example, but the actual tooltip-hover isn't affected by that as expected...