Can I programmatically confirm an email address

Sure, it is explained in the module's main page

launch an email confirmation in just 1 line
\Drupal::service('email_confirmer')->confirm('somemail@example.com');

I don't believe the question I asked is explained in the module's main page.

What wanted to build was a mechanism by which a user could confirm his email address by replying to the confirmation email sent by email-confirmer. I was looking for a hook that would allow me to do that.

I guess I wasn't clear enough in my question. Anyway, I came up with this process:

1. extract_confirmation_url_from_email($email_body)
3. extract_uuid_from_url($url)
5. confirm_email_by_uuid($uuid)

Here is the code I created to confirm the email address (using the code from the home page) using the uuid extracted from the reply email:

	/**
	 * Confirms an email confirmation entity by UUID.
	 *
	 * This method loads the email confirmation entity based on the UUID provided.
	 * If the entity is still pending, it marks the confirmation as confirmed, saves it,
	 * and returns 1 for a successful confirmation. If the entity is not found or 
	 * is not in a pending state, it returns 0.
	 *
	 * @param string $uuid
	 *   The UUID of the email confirmation entity.
	 *
	 * @return int
	 *   Returns 1 if the confirmation is successful, or 0 if the confirmation fails.
	 */
	function confirm_email_by_uuid($uuid) {
	  // Load the confirmation entity by UUID.
	  $confirmations = \Drupal::entityTypeManager()
		->getStorage('email_confirmer_confirmation')
		->loadByProperties(['uuid' => $uuid]);

	  // Get the first confirmation entity.
	  $confirmation = reset($confirmations);

	  if ($confirmation && $confirmation->isPending()) {
		// Bypass hash and directly mark as confirmed.
		$confirmation->set('confirmed', EmailConfirmationInterface::CONFIRMED);
		$confirmation->save();

		// Optionally invoke hooks or additional logic.
		\Drupal::moduleHandler()->invokeAll('email_confirmer', ['confirm', $confirmation]);

		// Return 1 for successful confirmation.
		return 1;
	  } else {
		// Return 0 for invalid, expired, or not pending confirmation.
		return 0;
	  }
	}

It's working.

I am aware that using this mechanism, all someone has to do is forward the email sent by email_confirmer to anyone they wish. But, in my situation, the onus for the results is on the user.

Anyway, thanks for the response. Better late than never.