They can be used for feeding your boilers and don't stop working when your power goes out, which helps for getting it back up.
Which is why when I read your description and saw that your mod makes them "uncraftable" it instantly killed my interest.
It's little short sighted to remove things because you think they don't have a use. There are creative ways of using all sorts of things.
Boilers without anything attached to them can be used to sort fuel because inserters that are pointed at them will only pick up fuel.
Underground belts that are approached by items from the side will allow through items on one side and and not the other. Which is good if you have coal on one side of a belt, iron the other, need that coal for your copper furnaces and can't risk contaminating your copper plate production with iron plates.

But I seem to have gone off on a tangent so I'll be brief: think carefully before taking things out ok?