Isn't the big problem that you have no idea what it's doing to your system? Also that you aren't expected to be able to undo it. You can read the makefiles, of course, but it seems simpler not to have to. (Just update the necessary packages yourself, to the latest version.)
Forgive me if this is naive of me.
As opposed to what exactly? Any other alternative, e.g. separate shell scripts, "npm run" scripts in package.json, running a Docker image, hell even cmake or other make-like tools - does stuff you don't know about without reading the files either.
I tend to write my Makefiles to create as much of a local dev environment as possible for every project. Using Python virtualenv/Pipenv/Poetry, Ruby vendored dirs, custom Gopath per project (using direnv), etc. Most tools support some sort of isolation/localisation, but it's often just not on by default.
I have seriously considered hiring someone to audit and prune all the random little libraries and tools I've installed over the years for that one-off time I had to process a weird file format or wanted to try something from HN.
It does sound like the right idea. This is hypocritical as someone who doesn't use it but I hope more people use it.
Every boot is a fresh install. Any one-off only becomes persisted unless I add it to my recipes.
At that point, I use a scripting -not shell- language (which is not as implicit)
I don't program in c anymore, so my major workflow is all in one language; I write my server in the same language that do s the compilation, which is in the same language that does utilities like creating network tunnels to my lab nodes