It's probably less about MS and more about the people downloading the packages

For them it is 5% of something tiny.

Maybe, maybe not. If you are on a bandwidth limited connection and you have a bunch of NPM packages to install, 5% of an hour is a few minutes saved. It's likely more than that because long-transfers often need to be restarted.

A properly working cache and download manager that supports resume goes a long way.

I could never get Docker to work on my ADSL when it was 2 Mbps (FTTN got it up to 20) though it was fine in the Montreal office which had gigabit.

The amount of modules my docker hosts download from npm is anything but tiny.