I don't think so. The source code is the same but there's now metadata that helps in setting up the same environment again, even years later. You still have the original code in case, e.g. Docker is no longer available.
For instance, if you just have a Python script importing a statistical library, what version are you going to use?
Scipy had a pretty nasty change in one of its statistical functions, changing the outcome of significance tests in our project. Depending on which version you happened to have installed it'd give you a positive or negative result.
It makes sense that having more information is better than less.
I would argue that they should use no dependencies to avoid this problem entirely, or download them and include them as source in the project, or at least include a note of which version of a major library they used in a README or comment. I think this is what is often done in practice currently.
Perhaps as you are saying, docker is just a stable way to document this stuff formally. But it is a large moving part that assumes a lot of stuff is still on the internet. What if the docker hub image is removed or dramatically changed? What if that OS package manager no longer exists? It just doesn't seem like our software is getting more longevity, but less. I don't know why we would bring that extra complexity to academic research if the goal is longevity.
For instance, if you just have a Python script importing a statistical library, what version are you going to use? Scipy had a pretty nasty change in one of its statistical functions, changing the outcome of significance tests in our project. Depending on which version you happened to have installed it'd give you a positive or negative result.