IMHO it would make sense to only have the productivity module effect stuff produced from raw materials.
Being more efficient when using e.g circuits doesn't really make all that much sense.

Yeah, pump running "for free" is a bit strange. We might do something about this. Maybe have it run on electricity but also put a small burner inside for the kickstarting. Wouldn't it be easier to have two different pumps, one for using only coal and providing little water and other running on ...

Notice I never said it would need electric power

Just as one can magically burn coal for making inserters move there could be a low-end pump that burns stuff to move water. Perhaps require two such pumps to fully feed a single steam engine?

Feel free to skip the spoiler part, it just describes where I come from :)
I've not played the game a whole lot yet but the little I've seen it seems to have tremendous potential. I especially like the way one has to run stuff through various machines to get final output. I also play a whole lot of ...