I had the exact same experience with layered architectures like described in this article. Avoid them as much as possible, naive and simple code is often better. It might look messy on the surface, and the layered code might look much cleaner. Until you drown in indirections, that are impossible to keep track of.

We've only made good experiences with layered architecture (onion architecture in particular, which is quite straight forward). We also never built it with the idea in mind to ever replace the storage engine. No, the big, big benefit has been that we can test everything without ever mocking a single class.

I also don't get the point about "going back to IoC" ... how is that mutually exclusive from using a layered architecture. This section was weird and didn't offer any good alternative.

It seems like some engineers have emotional attachment to all these layered architectures. Explaining or giving them examples of failed projects (based on this architecture) doesn't help.