The point of the article is that Hart is trying to stimulate a better-informed, less reactionary dialogue about these drugs.

it is easier to demonize less popular drugs such as crack cocaine and methamphetamine, which in the public mind are still linked, as marijuana once was, with addiction, madness, and violence.

He isn't recommending meth, just trying to get people to try and separate drug from person from environment and realize that these all play a role in how a user interacts with a drug.

His studies found that cocaine and methamphetamine do increase heart rate and blood pressure, but the effect of typical doses is not dangerous in otherwise healthy people. He argues that research linking meth to brain damage confuses correlation with causation and fails to show that meth users’ cognitive capabilities are outside the normal range.

The aesthetic appearance of chemical structure has absolutely nothing to do with the effect of a drug.

This is true and there are indeed important distinctions between the two drugs, but the similar structure is what causes them to have such similar effects. His point in saying they have the 'same effects', likely an exaggeration not to be found in his published work, is to emphasize that the violence and insanity often associated with meth is much more related to the circumstances of its use, not inherent properties of the drug itself.

As for why he didn't include heroin, it seems he's just focusing on amphetamines and the specific set of misconceptions about them. Heroin doesn't bring to mind the same picture of an amphetamine-fueled maniac. It's true that meth and heroin are probably pretty close on the addiction and life-destroying side and ideally he would discuss opiates in general as well, but it seems to me he's just focusing on what he knows and on doing one thing at a time, rather than trying to explain these complicated and controversial topics at once, potentially confusing his audience.