> apt/dpkg and any other package manager that scatters files all over the filesystem is just an absolute disaster that--if you do a lot of R&D tinkering--eventually renders a computer unusable after a few years.
That was your experience. Mine is that after using apt for a lot of R&D tinkering for 3 years, everything runs fine. apt is global. Sometimes that's great and that's what you want. Sometimes it's not. Another way to keep that in mind is to think as apt as "bad at doing cleanup".
The thing is that you have to have a separation between things that you want on your system all the time, and things that you use for one or more projects. For the first, apt is perfect. For the second, usually that's where I use tools like nvm for node versions, languages package managers like npm, and also docker (which I use a lot for development databases).
For a backend JS project, I would install nvm, npm and docker globally, and then for the project I would use node through nvm with a .nvmrc, install packages locally with npm and use a package.json and package-lock.json, and run the development database with docker through a npm command, usually the latest PostgreSQL version. The link between the backend and database would be made with environment variables, because that's also what I use in production.
The difference between the global (apt) scope and the project (the rest) scope might seem like a failure of apt, but I personally see it as the difference between global and local scope in programming: both have their use, we separate them for a reason and we don't put the same things in them.