I've been out of the industry for awhile, and skimmed through the article, and I don't know that either of the problems would occur. It really depends how the idea is turned into a specification, as approved by a standards body from industry.
The way QoS works for VoLTE for example, is not by putting application layer knowledge at the link layer. Instead the services that activate and route a phone call, have the ability to send a rule, called a traffic flow template, to the underlying LTE network. The flow template is a description of a flow from/to the device, that then has the transport network apply the expected scheduling behavior. I want a guaranteed 15 kbps for real-time voice, the LTE network can then use to coordinate radio scheduling, prioritize against background bulk transfers, block handoffs to cell towers that wouldn't have enough capacity, etc.
In concept this would work with fully end to end encrypted video and chat (I left the industry before the encrypted side was rolled out). I suspect some might argue the flow template itself leaks information about the data, but an observer of the network traffic can likely glean similar information, a steady flow of small packets is probably voice traffic type of idea. This just gives the network enough information to identify a flow and control for how to schedule the packets.
The biggest restriction is rollout and integrating with external services. Needs agreements between companies, restrictions on abuse, etc, etc.
Anyways, I don't think what is being proposed necessitates the problems. It'll really depend on what the standards bodies decides to do.