VS2012 - Web Forms - Bundling Confusion
Solution 1:
UPDATE: This is a new blog post which also talks about this more: ASP.NET article
Basically webforms + bundling looks like this due to a bunch of legacy behavior that we weren't able to change in scriptmanager.
In regards to your specific questions:
Basically this is so deduping works correctly, script manager has a limitation for the origional script resources which prevents them from being scriptmapped, so they need to be mapped to disk which then gets properly deduped because the files are already included in the bundle. The WebformsBundleJs is a script mapping that is created inside of the PreAppStart code inside of the ScriptManager nupkgs. (I agree this is nearly impossible to discover)
New 4.5 features like unobtrusive validation required jquery(via scriptmanager), which is why script manager was used to ensure jquery doesn't get rendered out twice.
This will work fine, but it will never dedupe with ScriptManager. So for modernizr it won't be an issue.
The jquery packages drop the jquery files to disk in your Scripts folder.
That reference pulls in the msajaxbundle which contains all of the ajax scripts, if you don't need/want them, I think its safe to remove.