If your makefile fixes up a file using sed and your system has gnu sed, your makefile may fail on a system with BSD sed (e.g., a mac). If you rely on bash-isms, your makefile may not work on a debian system where it will be run with dash instead of bash. And so on.
If you look in your package.json, you'll surely see a dozen or so "scripts" lines that run through the same shell that make does and have all the problems you just mentioned.
I'd also like to point out that Linux and almost certainly your production environment (because it's most likely *ix) will be case sensitive. Your macOS or Windows file system? Not so much. Point is, you're already up to your neck in portability issues. My macOS coworkers often forget this detail.
huh?? No it's not. That's the whole discussion we are having now. I even specifically mentioned my macOS coworkers who develop on their Mac and are oblivious to case-sensitivity issues. Because "it worked for me."
> If an external package has scripts in it, those scripts have very likely been run by somebody on a mac and somebody on linux and worked in both cases.
Oh, I'd love for that to be true. But also not what I was referring to. Most large projects have a "scripts" section and those are no different than Makefile commands. If you're paranoid about your own Makefiles then you're going to need to be paranoid about your own package.json.
Also, I use javascript where it makes sense: I rely on Browserify to resolve the web of `require`d files.