Very often they do. Many of these internal applications are from mainframe computer times when interacting with applications exclusively via the keyboard shortcuts was the norm. In most companies, they never dared to remove those because the Power Users are used to them for decades.
Problem is, few people are trained directly by those power users so they never learn those efficient shortcuts. And they are never well documented.
In the railway context an engineer was the person who worked the engine.
In German the word comes from Latin roughly meaning inventor. Presumably the general usage of the word engineer in English has the same etymology.