I do think that the current PhD system is broken. As pointed out very correctly in a comment above: "I believe the problem lies in funding. Currently, we base funding largely off of publication success."
However, all is not lost. I have made a conscious effort in my PhD to not end up super specializing. I have tried to take up a problem that requires me to learn about multiple different computer science areas (compilers, architecture, machine learning and graphics currently). This has made my PhD a lot harder as I have to spend considerable amounts of time reading while others are publishing papers and getting better scholarships, I do think this is better for me in the long term.
Overall, while I no longer recommend anyone else to do a PhD, on the flip side if you work hard enough you might still gain value out of a PhD. Whether that value is enough is debatable, and requires considerable effort, but it is also possible to not super-specialize by picking your research topic wisely.
I do agree with the article in general and do think that more cross disciplinary stuff needs to happen. The academic system is currently largely unsympathetic towards trying to cover multiple sub-areas even within computer science with people in other sub-areas often being unwelcoming. Funding agencies are also unhappy with the much larger "startup time" spent in cross-disciplinary projects during which you spend time reading and not publishing.