The hook woocommerce_email_order_details has 4 parameters which can help you to identify the correct message.
add_action( 'woocommerce_email_order_details', 'so274215_add_transaction_id', 10, 4);
function so274215_add_transaction_id( $order, $sent_to_admin, $plain_text, $email ){
// decide here wether to show your transaction id
if ( ! $sent_to_admin )
echo '<span style="color:#555;font-size:1.5em;">Transaction ID: '.get_post_meta( $order->id, "_transaction_id", true ).'</span>';
}
As far as I remember the last parameter $email contains the name of the current message, just in case you want to go more into detail.
if( 'WC_Email_Customer_On_Hold_Order' == $email ) ...