A plant shutdown at 100ppm will likely result in running the plant at 90ppm to account for the risk of breaching the limit. But if I only pay an extra $100/min when run at 100ppm I'm better off running at 99ppm and just paying the extra tax when I occassionaly exceed 100ppm.
In your example, the tax incentivises you to pollute to the point you can afford. It might be cheaper to just pay the tax than actually make the required changes to your process.
However if the regulation sets a strict limit you don't have a choice, you have to make the changes necessary to comply with the regulations.
To the author's original point, it is important to look and what you are trying to achieve and why. In some cases tax incentives/penalties will make sense. In others strict limits/bans will be required.