And that's what a PhD is: it's a vocational degree coupled with an apprenticeship. It's not like a BS or MS: it's ultimately not about courses or grades. Rather, you are attaching yourself, like a barnacle, to a researcher -- the professor -- so that you can learn how to be a researcher yourself. Eventually you step out from under her wing and do some research on your own, and that forms your thesis work.
You could learn to do research in a specialized field without going through this process -- and I know several who have -- but you'll probably discover along the way that science or engineering research is an apprenticeship field for a very good reason.
note that a PhD in a computer science department is going to be much less bad than the humanities PhDs described in the article.
- they are fully funded, stipends are somewhat higher (at least not total starvation level), and there is the opportunity for lucrative industry internships
- students in general have leverage, because it's possible to leave and go get a high paying engineering job
- there's a bias towards continuing in academia but it's not taboo to go to industry; you don't have to lie about this.
- for a combination of these and other reasons, i don't think an abusive culture has set in: professors don't feel like they need to haze their students.
i don't mean to imply that everything is beautiful and perfect but it is way less culty.
While I don't do academic research, I spend a non-trivial amount of time reading papers and keeping abreast of new research that is relevant to my job. If the research seems relevant enough, I'll dig deeper and implement the research into a workable model. The software engineering portion really kicks in when I productionize this model and make it a usable product.
So in regards to your question, if you want to do fundamental, academic research then go for your PhD. For the kind of work I do currently, then it's more about the group you work with in industry.