I agree. Especially Flatpak and AppImage facilitate this goal.
I do run some software that communicates with the internet in a bubblewrap sandbox, like Chromium and Transmission, but other than that I shouldn't have to run every piece of software in a container to be safe.
That's easy for companies since they deal with "standard" "Ford model like" people, but that's a killer for evolution especially evolution driven by people/users, not upstream/companies.
If you can tailor software to fit your needs as you like you get a friendly personal environment and you have "a bit of power" on society, you still need upstream work but you are also a bit independent, and the same is for upstream to have help from the community they need to comply with an heterogeneous community with users, not consumers. We are in the end interdependent so forced to cooperate in a relative peace. On the over side we totally depend on upstream being effectively powerless. Oh yeah, you can choose different software, at least for now, but that need to exists, that's no more a community.
A simple example a proprietary software, Master pdf editor, gain a bit of success in GNU/Linux world and decide to insert watermark on modify pdfs by free version. If it's distributed by single distro, single distros can keep old version for long time. Leaving all needed time to their user to switch. If you relay direct on upstream you discover the new "feature" a day perhaps without warning because it's auto-updated for instance, and you may have no time, no choice. This also happen recently with the "tweaked" Android settings by Google and I think many many other cases.
Freedom it's not only "being free of doing something" it's also can do something easily, have a system that let you be as free as you like.
Example: I used to work at a place that, for a variety of reasons, needed to use custom builds of upstream Debian packages. So, we created our own Debian container base and rebuilt all the major Docker container "base" images (e.g. `openjdk`, `python`, `node`, `nginx`) with our own image as base. We had custom control all the way down to the OS level, and our orchestration solution (Kubernetes in our case, but a pile of shell scripts calling LXC directly works too).
I totally get being skeptical of {Docker|Kubernetes|Mesos|GKE|EKS|AKS}, but there's nothing inherently "un-free" about containers. They're a nice packaging primitive that happen to have some (useful, but not mission-critical) security features bundled in. So, your whole point kinda confuses me. That containers are standardized by OCI/LXC just makes them easier on your poor sysadmins to administer than 100 engineers' pet servers each running a different version of Emacs.
Think about the level of integration of Emacs and it's flexibility vs Eclipse/VSc/... the former is completely integrated and you can essentially modify any aspect at runtime with a simple sexp/config change. While the letter require to write and maintain plugins. The burden between programming and using in Emacs is substantially nonexistent, while you feel it on any modern software.
I do not know if it's clear seeing my bad English but I hope so. Think another example, Xerox model Alto&other Smalltalk machines, freedom it's not only the code but the way you use and customize your system, it's simplicity and flexibility. In FOSS we are all a bit devs, a bit admin, a bit users, a bit ..., while in proprietary world anything is rigid compartmentalized and "switch" between compartments it's not easy. The very same concept apply to containerization of software.