An example of how to include conditional tags within the messages system

functions.php

<?php
//Do not include the opening PHP tag if you already have one.

function tw_ee_register_template_shortcodes( $shortcodes, EE_Shortcodes $lib ) {
  	
  	//Which sections of the messages system do we add the shrotcodes.
	if ( $lib instanceof EE_Datetime_Shortcodes || 
		 $lib instanceof EE_Event_Shortcodes || 
		 $lib instanceof EE_Registration_Shortcodes ||
		 $lib instanceof EE_Transaction_Shortcodes ||
 		 $lib instanceof EE_Attendee_List_Shortcodes ||
		 $lib instanceof EE_Ticket_List_Shortcodes
		) 
	{
		//Add custom shortcodes here.
		//The shortcode is the key, the 'help text' is the shortcodes value.
		$shortcodes['[if gte mso 9]'] = _('Testing template shortcodes');
		$shortcodes['[endif]']  = _('Testing template shortcodes');
		$shortcodes['[if mso]']  = _('Testing template shortcodes');
		$shortcodes['[CUSTOM_SHORTCODE_*]']  = _('A custom shortcode that outputs whichever text after the * in a shortcode');
	}
	//Return the shortcodes.
	return $shortcodes;
}
add_filter( 'FHEE__EE_Shortcodes__shortcodes', 'tw_ee_register_template_shortcodes', 10, 2 );

function tw_ee_parse_template_shortcodes( $parsed, $shortcode, $data, $extra_data, EE_Shortcodes $lib ) {

	if ( $shortcode == '[if gte mso 9]' ) {	
		return '[if gte mso 9]';
	}
	if ( $shortcode == '[endif]' ) {	
		return '[endif]';
	}
	if ( $shortcode == '[if mso]' ) {	
		return '[if mso]';
	}
	if (strpos($shortcode, '[CUSTOM_SHORTCODE_*') !== false) {
		$shortcode = str_replace('[CUSTOM_SHORTCODE_*', '', $shortcode);
		echo $shortcode;
		$shortcode = trim(str_replace(']', '', $shortcode));

		return '[' . $shortcode . ']';
	}
	return $parsed;
}
add_filter( 'FHEE__EE_Shortcodes__parser_after', 'tw_ee_parse_template_shortcodes', 10, 5 );