How does MVC4 optimization allow partial view scripts?

One thing you can do is create some HtmlHelper extension methods like the following:

using System.Collections.Generic;
using System.Linq;
using System.Web;
using System.Web.Mvc;
using System.Web.Optimization;

public static class ScriptBundleManager
{
    private const string Key = "__ScriptBundleManager__";

    /// <summary>
    /// Call this method from your partials and register your script bundle.
    /// </summary>
    public static void Register(this HtmlHelper htmlHelper, string scriptBundleName)
    {
        //using a HashSet to avoid duplicate scripts.
        HashSet<string> set = htmlHelper.ViewContext.HttpContext.Items[Key] as HashSet<string>;
        if (set == null)
        {
            set = new HashSet<string>();
            htmlHelper.ViewContext.HttpContext.Items[Key] = set;
        }

        if (!set.Contains(scriptBundleName))
            set.Add(scriptBundleName);
    }

    /// <summary>
    /// In the bottom of your HTML document, most likely in the Layout file call this method.
    /// </summary>
    public static IHtmlString RenderScripts(this HtmlHelper htmlHelper)
    {
        HashSet<string> set = htmlHelper.ViewContext.HttpContext.Items[Key] as HashSet<string>;
        if (set != null)
            return Scripts.Render(set.ToArray());
        return MvcHtmlString.Empty;
    }
}

From your partials you would use it like this:

@{Html.Register("~/bundles/script1.js");}

And in your Layout file:

   ...
   @Html.RenderScripts()
</body>

Since your partials run before the end of the layout file all the script bundles will be registered and they will be safely rendered.