Redundant would imply they aren’t needed.
I’m assuming that they are still needed (afterall, you want to put them in), but you mean you want to insert them at build time?
If you control the back end generation of the page, that’s not difficult.
The current site I’m working on uses a boilerplate page template that looks like this:
<!DOCTYPE html>
<!-- PHOTOGRAPHY, DESIGN AND CODE BY MICHEAL HALL ... I'VE LOST COUNT OF HOW MANY TIMES I'VE BUILT THIS SITE O.o -->
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<!-- Required meta tags always come first -->
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta http-equiv="x-ua-compatible" content="ie=edge">
<meta name="description" content="{{meta-description}}"> <meta name="keywords" content="{{meta-keywords}}">
<title>{{page-title}}</title>
{{css}}
</head>
<body data-pagename="{{pagename}}">
{{navigation}}
<div class="container-fluid carousel_container slide_up hidden-sm-down" data-mediadisplaybreakpoint="hidden-sm-down"></div>
<div class="container body"></div>
<div id="footer" class="footer container-fluid">
{{footer}}
</div>
{{fragments}}
{{js}}
<script>
$( document ).ready( function(){
UTILS.initialize_page();
});
</script>
</body>
</html>
Simple, small, contains just the barebones common to all pages needed by the site. The rest are tags replaced during site build with content appropriate to the page.
Depending on a build switch, the
{{css}}
{{js}}
tags are replaced with style and script tags which either point to a localhost or to an online CDN.
During development, where I may not be online, I use my local, non-minified copies. When I’m done, I’ll change the switch and build the site using the CDN hosted, minified versions before I upload it.
What replaces the js and css tags is controlled by a site configuration file.
But you have to control the back end build yourself. On my end, I’ve written myself a command line tool I can use to automate all of my page building/outputting, image resizing, etc., etc.
As you’re a back end guy, I imagine it wouldn’t be all that difficult to accomplish.
A final thing to consider is whether or not those script tags are inserted where they are for performance reasons. JS loading/parsing is blocking and it’s generally considered best practice to put your JS at the bottom of the body tag so that all CSS and page content can load without blocking and the JS hits the page at the end.
But, if you need the JS to execute as soon as possible, you can insert it right where it’s needed in the page, and it will execute as the page is loaded and parsed.
Only you can say if that is why those script tags are where they are. If you move them and the page breaks or looks crap when loading, you’ll have your answer. 
~Micheal