Ah from that perspective I can see how this might appear to be better. Personally, I like the 'magic' of NPM (which to be honest I don't really think is all that magical, it's quite transparent what's happening behind the scenes). This 'magic' means I no longer have to write 200 line makefiles, so it definitely makes my life easier.
You can use lock-files, bundles, and many other features that makes dependencies management easier.