IIRC, there is a jQuery global object available.. you can assign it to a local variable inside in iife, which is the appropriate way to use jQuery when writing a module...

    (function(window,$){
      //module code goes here
    }(this.self || this, jQuery));

In this way, you are keeping jQuery itself and your implicit scope assigned to localized variables.

If you are writing a modern module (not necessarily jQuery based), then following node/cjs conventions is probably best. If you use this convention with such a plugin, said module should probably return the jQuery object that has been modified, and extra care should be taken that all plugins are using compatible/same instance of jQuery.

What modules? You mean CommonJS or was it AMD or ECMAScript 6? Still a straw man IMHO :-)

CommonJS, since npm (which is mainly commonjs) is a few hundred/thousand times larger than the whatever else.