So, he clicked the link and then entered his correct TOTP? how would manually typing the url instead of clicking the link have mitigated this?
They wouldn't have manually typed the exact URL from the email, they would have just typed in npmjs.com which would ensure they ended up on the real NPM site. Or even if they did type out the exact URL from the email, it would have made them much more likely to notice that it was not the real NPM URL.