Exclude all AMP scripts from being moved to the footer by the Scripts To Footer plugin. All AMP scripts have async anyway so they do not need to be moved to the footer for performance.

scripts-to-footer-exclude-amp.php

<?php
/**
 * Plugin Name: Scripts-To-Footer Exclude AMP
 * Description: Exclude all AMP scripts from being moved to the footer by the Scripts To Footer plugin. All AMP scripts have async anyway so they do not need to be moved to the footer for performance.
 * Author Name: Weston Ruter
 * Plugin URI: https://gist.github.com/westonruter/90c8cbfd9cb4d3882a461b5e71aa10e5
 */

add_filter( 'stf_exclude_scripts', function( $scripts ) {
	return array_merge(
		$scripts,
		array_filter(
			array_keys( wp_scripts()->registered ),
			function ( $handle ) {
				return 'amp-' === substr( $handle, 0, 4 );
			}
		)
	);
} );