I agree that if you use Rails and constantly override its conventions, you will have a bad day. But following conventions is usually a strength, not a weakness. Most websites are not shocking cutting-edge things that have never done before, but relatively boring simple tasks that involve grabbing data from databases and showing them to users via templates. Every decision you have to make is a cost, and if you have a small team, having basic naming convention decisions and directory location decisions already made accelerates development. There's a big advantage to following conventions when you want others to work with you, because different Rails applications look quite similar in many ways.
I have not had trouble overriding Rails when I needed to override something specific.
Btw, I like the original article. There's nothing that's good for all cases, so it's very important to understand what something is good and not good at.