The author's idea is that this short term gain damages longer term metrics. That sounds logical and agreeable, but that doesn't make it true. Not in my experience anyway.
Probably the people complaining the most about annoying UI patterns weren't going to convert anyway. Whilst those coming with a specific conversion goal to your site will convert even if annoyed in the process.
Anyway, the true root cause goes all the way to the top. When you give a team a 20% sales increase target and "deliver by next quarter or be fired"...this is what you get. If the executive level dismisses a healthier, more sustainable long term growth model, then there's pretty much no way to stop this.
It's so hard to stop because it actually works. It works short term and evidence that it harms long time is typically lacking or it simply isn't true.