I might be misunderstanding you alignment comment but it seems to me the only relevant alignment is to the receiver module which is connected to the relay module input. It doesn't matter what the module that is only acting as a emitter is doing as a receiver. I wonder if that makes sense.
Anyway, a capacitor connected at the input to the relay module might eliminate the caboose flicker issue. If you have a capacitor in the 100uF range (16V or more), connect the + side of the cap to the relay module input, and the - side of the cap to Ground/common. You can try larger values if that's all you have. But you only have smaller values don't bother with anything below, say, 10uF which would have no meaningful effect. A simple capacitor is certainly expedient but will give you delays or flicker tolerance in the fraction of a second range (which can be remarkably effective). If you're look for delays in the seconds like with an ITAD delay you need to use a more complex circuit (3 or so components) as shown in the linked threads.
A soda straw which just happens to slide over the emitter is another high-tech alignment "tool." 
