I'm not sure there's an easy way to explain it. As it stands assemblers are "black boxes" where you put things in and new things come out. The nuances are not visible to the player and in truth they kinda never were. And before you say "yes they are" then tell me what this factory does. Or this one. Or this one. Notice a common theme? Without the all powerful information overlay active, you're almost completely blind. I think the information overlay has been a gigantic crutch for essentially all of development and no real game testing has been done without it. Even on the factorio guides one of the first steps for the player is "turn the UI on" because it's nearly impossible to play without it.As for ingredient limits being "yet another thing that had to be explained somehow," explain that the simpler machines are more limited in functionality, and can only craft simpler recipes.
I think a big problem here feeds into the the important early game experience of "show don't tell". Players have a finite patience and it is more fun to watch things happen than to read about what should be happening. Some aspects of Factorio are handled extremely well in this regard. Mines do mining, belts do belting, and inserters swing around and it's a lot of fun to watch it all in action. Simple devices show simple feedback, but assemblers aren't very simple. They contain a lot of important information such as recipe, resources and activity and most of that information is critical to the gameplay at all times. So before telling me what the key essential difference between these three assemblers is: Maybe it'd be more constructive to see how the default feedback on their function can be shown in a better way?
With the video engine getting super optimized I think it's a great time to discuss how maybe things could fit better into the game's "natural" view. That way things can both look and play well without having to bury the experience in overlays. Maybe I'm talking crazy, but an overlay should help enhance the experience rather than being the core essentials.