noscript tags are being commented-out

This is working as intended. Custom JS is not allowed in AMP (unless using amp-script), and will be removed. Thus by default activating AMP with a theme will cause it to behave as if JS is turned off in the browser. To improve the graceful degradation process, in addition to removing custom scripts it will also unwrap noscript elements so that their content becomes the AMP version by default.

You can see the logic here: https://github.com/ampproject/amp-wp/blob/bf8dfc88442a3e66139621ede9f4ccd5bc754c34/includes/sanitizers/class-amp-script-sanitizer.php#L51-L66

I’m noticing that you’re using the amp-gist component in a non-AMP page. What you can do is simply put the noscript inside of the amp-gist. Like so:

<amp-gist data-gistid="400f4d0338a306c5e6db8c1819e78d5d" layout="fixed-height" height="303">
	<noscript>
		<code>
		add_action( 'admin_head', 'set_admin_ip' );
		function set_admin_ip() {
			$current_admin_ip = $_SERVER['REMOTE_ADDR'];
			$saved_admin_ip   = get_transient( 'saved_admin_ip' );
			if ( ! $saved_admin_ip || $saved_admin_ip !== $current_admin_ip ) {
				set_transient( 'saved_admin_ip', $current_admin_ip, 12 * HOUR_IN_SECONDS );
			}
		}
		</code>
	</noscript>
</amp-gist>

When noscript appears as a direct child of an AMP component, the unwrapping behavior is prevented. See source.

Feel free to leave the plugin a review!