The options in VS for exceptions to determine if the debugger should break on an exception. Though VS will always break on an unhandled exception and a language break (debugger). The options do not stop the script debugger from being attached when you launch IE from VS.
The options in VS to enable or disable JIT debugging change just the just-in-time debug feature. Enabling JIT debug simply means that if a running application not launched by VS hits a break condition the user should be prompted if they want to attach VS to debug the application. This also don't change if script debugging is enabled when you launch IE from VS.
The options in Internet Explorer to disable script debugging only changes if IE should run with debugging enabled always. In IE11 with VS2013 this feature is never needed but is there to support older versions of VS.
The easiest way to get the behavior you want is to do:
1. Right click on a aspx/html file there is a ‘Browse with…’ item. This will bring up a dialog to configure your browser.
2. Click the Add button. Add something like:
Path: c:\Program Files (x86)\Internet Explorer\iexplore.exe
Friendly name: Internet Explorer (no debug)
3. Set that as your default