This whole Nuget/update version model in JQuery is a huge mess! (Who designed this system?)
What I do is simply avoid the JQuery template piece in Visual Studio and place the current JQuery javascript links in ONE PLACE in your web project so its pasted into every single page......either the MVC Layout page, usercontrol, or masterpage. You can mix and match controls. But it doesnt matter as modern browsers cache these files after the first download anyway.
Now when you do a JQuery update, you can fix it in one simple place in your web project. All ECMAscripts have been done this way anyway the past 15 years using server side includes or other strategies. I'm still not sure why you want a template to stuff links in hundreds of view pages in MVC you now have to customize one by one when you get different versioned files names. I think ASP.NET MVC has gone backwards in its design for that reason.