Base metabolism doesn’t change much for an average body size of a human being. It does change a bit with more lean muscle tissue but not much. The amount of required calories you burn working, “forcing” your body to go through painful transformation, will increase because on a daily basis, you need more nutrition to recover and more glucose to do the work, so it will increase with high level endurance training. But base metabolism will go right where it was once you stop training. What the article talked about was base metabolism for a lifestyle of an average man or woman who are not into advanced weight training but more into NON challenging treadmill routines type of training. And junk obviously never leaves the body without negative effects.
I had to do some research to figure out what exactly the researchers were talking about because obviously a pro-bodybuilder or elite marathon runners etc. do need more nutrition and energy.