It appears this issue is fixed in npm v5.4.2
https://github.com/npm/npm/issues/17979
(Scroll down to the last comment in the thread)
Update
Actually fixed in 5.6.0. There was a cross platform bug in 5.4.2 that was causing the issue to still occur.
https://github.com/npm/npm/issues/18712
Update 2
See my answer here: https://stackoverflow.com/a/53680257/1611058
npm ci
is the command you should be using when installing existing projects now.