Scripts don't belong in the head of your document. They belong at the bottom of the page, before the closing body tag. As of 2.3 that's where they should be going. If it's not doing that, there's certainly nothing invalid about including the scripts outside of the head. But as a general best practice, you really want them at the bottom of your document, below all the structural markup.
Even if it's best practice to optimize loading times by putting your js files at the bottom of the page (btw, you can specify "defer" if you put your scripts in the head, it will already help a lot), it may have some side effects. For example, if you use a library like swfobject, you may see the content that is about to be replaced. Or if you use libraries like jquery, all your behaviours on your page may not be working properly until the library is loaded.
I guess it would be nice if it was possible to choose to include the scripts in the head or just before the body closing tag.
+1 again for being able to choose <head> or <body> on a per-file basis. I'm big on best practices, but there's usually a script or two I need to put into the head to avoid the aforementioned content flash issue.
+1 again for being able to choose <head> or <body> on a per-file basis. FOUC related JS like modernizr or prefixree js should be after the CSS in the head, where as jQuery and other plugins should be don't in the body.
Even better if I could put a variable into my template for exactly where I want it to go in case I want to place something after the JS/CSS in the head but before the closing </head> tag and same goes for the </body> tag. This would also save you from HTML parsing for the placement.