Thanks for pointing it out. I couldn't figure this out on my own.
I ended up doing it this way using node path

module.exports = Encore.getWebpackConfig();

let config = Encore.getWebpackConfig();
config.resolve.alias = {
    'jquery': path.join(__dirname, 'node_modules/jquery/src/jquery')
};
module.exports = config;

that's because a jquery plugin should actually have a peer-dependency to jquery, not a dependency (as it wants to alter the dependency used by the requester instead)

Yea, so really, if we decide to fix this, it’s because we’re working around a bug in some js library that has done this incorrectly.

anyway, if you have multiple jQuery copies locally, because some plugins are not declaring their dependencies the right way, you cannot always fix this with an alias (what if they are incompatible versions ?).

So this should get reported to the package.