For many systems, the application and the machine are so intertwined as to basically be the same thing.

A lot of web apps are just boring CRUD APIs. The business logic behind these is nothing special. The differentiating factor for a lot of them is how they scale, or how they integrate with other applications, or their performance, or how fast they are to iterate on, etc. The “machine” offers a lot of possibilities these days that can be taken advantage of, so customizing “the machine” to get what you need out of it is a big focus for many devs.