Your Content belongs to you. You decide whether and how to license it. But at a minimum, you license npm to provide Your Content to users of npm Services when you share Your Content. That special license allows npm to copy, publish, and analyze Your Content, and to share its analyses with others. npm may run computer code in Your Content to analyze it, but npm's special license alone does not give npm the right to run code for its functionality in npm products or services.
First you agreed to ToS when you uploaded things to npm. I haven't read the terms but it should be enough for npm to publish on npm no matter the license.
Secondly and as important if you publish something under an Open Source license(1) then you _cannot
unpublish it_. You granted copyright to
_everyone_ for and existing both now and in the future to distribute and use it(2) (legally it's a bit more complex but that's what it boils down to).
(1): Assuming you had the legal right to do so, but if not you are liable for any fall out, not npm (because ToS, they still need to take it down reasonable fast, but they might be able to sue you).
It is indeed all, even if you ignore the "popular" qualifier. If a license could be unilaterally revoked, it would fail to meet the Open Source Definition for that reason.
The differences between the two are extremely minimal, basically only relating to patent rights relating to the software. Go read https://www.gnu.org/philosophy/free-sw.en.html - the FSF's Free Software definition, and https://opensource.org/osd - the Open Source Definition (both by the respective parties that coined the terms and maintain them to this day) and see what the actual differences are. They're not many.
There is absolutely no copyright or publishing right transfer that takes place when one "publishes" a package on NPM (or on Github). None.
The original author is absolutely entitled to a DMCA takedown notice and NPM would have to oblige him.