The issue is not that they can tell which phone number you use, obviously. As I see it there are three problems with this kind of tracking technology:
Secondly, mass surveillance is not just about you as an individual. By looking at where you go when and how long you stay there and correlating this with who else goes there at the same time one can make deductions about social networks within society without ever looking at one person up close.
I am with you on abuse from repressive regimes. But when you say "with this technology", I fail to understand. All the uses and abuses you mention are already not only possible, but routinely done by repressive regimes, and some. "This technology" adds nothing to the equation, except perhaps marginal cases where they would want to track you "across devices".
In this regard, I can only find that the profound implications mentioned in the article are not so much profound as they are obscure.