Your question seems to be based on a false premise ("The javascript alert box always shows up at the top of the page"). Where a Javascript alert() box appears is down to the browser: from a quick test:
Chrome positions the alert box centred, at the top of the browser window:

IE11 positions the alert box in the centre of the screen (both vertically and horizontally), irrespective of where the browser window is:

This lack of control of the position and appearance of the built-in alert/confirm dialogs of Javascript is why many implement alerts using JS/CSS.
Answer from TripeHound on Stack ExchangeVideos
Yes you need javascript. The simplest way is to just put this at the bottom of your HTML page:
<script type="text/javascript">
alert("Hello world");
</script>
There are more preferred methods, like using jQuery's ready function, but this method will work.
You can use a variety of methods, one uses Javascript window.onload function in a simple function call from a script or from the body as in the solutions above, you can also use jQuery to do this but its just a modification of Javascript...Just add Jquery to your header by pasting
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.1.1/jquery.min.js"></script>
to your head section and open another script tag where you display the alert when the DOM is ready i.e. `
<script>
$("document").ready( function () {
alert("Hello, world");
});
</script>
`
This uses Jquery to run the function but since jQuery is a Javascript framework it contains Javascript code hence the Javascript alert function..hope this helps...
The alert box is a system object, and not subject to CSS. To do this style of thing you would need to create an HTML element and mimic the alert() functionality. The jQuery UI Dialogue does a lot of the work for you, working basically as I have described: Link.
<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>jQuery UI Dialog - Default functionality</title>
<link rel="stylesheet" href="//code.jquery.com/ui/1.12.1/themes/base/jquery-ui.css">
<link rel="stylesheet" href="/resources/demos/style.css">
<script src="https://code.jquery.com/jquery-1.12.4.js"></script>
<script src="https://code.jquery.com/ui/1.12.1/jquery-ui.js"></script>
<script>
$( function() {
$( "#dialog" ).dialog();
} );
</script>
</head>
<body>
<div id="dialog" title="Basic dialog">
<p>This is the default dialog which is useful for displaying information. The dialog window can be moved, resized and closed with the 'x' icon.</p>
</div>
</body>
</html>
I use SweetAlert, It's Awesome, You will get lots of customization option as well as all callbacks

swal("Here's a message!", "It's pretty, isn't it?");
