It would affect the everything package, but not the issue since the issue is caused by npm's policy + simply creating thousands packages with, say, 5 dependenci

It would affect the everything package, but not the issue since the issue is caused by npm's policy + simply creating thousands packages with, say, 5 dependencies that cover all of the module space. That they rolled all of those submodules into one big everything package is just a gimmick, not a source of the problem.