There's generally an entire phase of prototyping where engineers will be using production boards but still need JTAG, which is why it's fused and why these kinds of features exist. It's a lot easier to have your lower-level software team (drivers/BSP, perf, etc.) sitting with production-ready units provisioned with engineering keys and debug enabled than to have them having to use some kind of case-off JTAG header setup, cost aside.
JTAG also isn't usually exposed through enclosures, so using the probe on a field unit might require destructive entry depending on the application.
And I am not knocking JTAG over USB. It is certainly convenient and beneficial since you can enable it in production or deployed units. I was commenting on how the GP (and even article) was making it out to be missing capability. They just do not have the cheap tools that are the intended way to access that capability.
edit: The article even mentions how the "Qualcomm Landing Team at Linaro", which seems to be the team that works with pre-production hardware to get them working on launch day, has a development process where "debuggers have never been a staple of our work for all the typical reasons you'd expect (cost and complexity being the main ones)". That is literally the team that should have pre-production units in the lab which will have debug connectors and where JTAG probes should be par for the course, yet they are apparently hardly using them partly because of "cost".
Having read a lot of Qualcomm code myself, I don't envy their job.
Well, should be. I bet there've been screwups now and then...