Why would you need to only look at single core performance to compare apples to apples? Qualcomm can fit more cores in the same die for a lower cost (or is willing to charge less overhead, at least), providing a faster multicore CPU. Wirh everything from games to web browsers leveraging multiple cores these days, multi core performance is quite relevant.
Their performance may come at a cost of efficiency but they're beating most of the M series chips when it comes to raw CPU performance. Legacy software running only on a single core will be slower, but I haven't had a CPU core run completely idle while another is on high load for years.
Furthermore, this article is on modems, an area where Qualcomm rules and Apple has a lot to gain. I'm sure Apple will catch up eventually, but they're still catching up at this point and if Qualcomm has managed to apply the lessons they've learned from catching up with Apple in the CPU area, that may take longer now that Qualcomm has reason to be competitive again.