I came across a white paper from Canon that talked about the structure of the sensor. Every step in the process is designed with decreasing noise in mind. For the theory that there is no penalty the ISO Settings in camera must = the EV bar in LR.
This is a comment in your linked article:
"Upon comparison of the exposures, it’s immediately apparent that the Canon EOS 700D/T5i is not completely ISO-invariant"
This would lead me to believe that there are process in the camera that take place that are not completely replicated in LR.
Another article I was reading said that most Canon bodies are not all invariant.
This sounds like a rehash of the Sony DR argument / debate.