The main point of confusion in this whole thread is whether or not the article states you shouldn't apply themes on your own computer. To some, myself included, it kind of does. Linux distributions are not individual operating systems - they're essentially skins on top of Linux kernel, created bottom-up to offer opinionated choices to users. Picking a distribution is like modifying software on one's own computer, except without duplicating the same work other people would do. In this sense, the article does ask users to not customize software on their own machines.