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And where is the problem?
You have a function for displaying content, the form getContent ().
Add your own div to this feature.

https://devdocs.prestashop.com/1.7/modules/creation/adding-configuration-page/

public function getContent()
{
	$output = '';
	$output .= '<div class="alert alert-danger" role="alert">'.$this->l('here is top alert message').'<div>';
      
	return $output . $this->displayForm();
}