Making a broad but concrete+simple interface to event registration + contributions + memberships. A few simplifications (which seem acceptable): there's no need to create arbitrary line items; line-items are only created in the context of a participant/membership/contribution. At most, you might tweak the line-item that's autogenerated.

ex.php

<?php

interface CiviInvoice {

  /**
   * Add details about a registration which a constituent would like to purchase.
   *
   * @param Participant $participant
   *   The event-registration which would be purchased.
   * @return LineItem
   *   A new line item which represents the would-be registration.
   */
  function addParticipant($participant);

  /**
   * @param Contribution $contribution
   * @return LineItem
   */
  function addContribution($contribution);

  /**
   * @param Membership $membership
   * @return LineItem
   */
  function addMembership($membership);

  /**
   * @param Payment $payment
   */
  function addPayment($payment);
  
  /**
   * @return array<LineItem>
   */
  function getLineItems();

  /**
   * @return LineItem
   */
  function getLineItem(int $lineItemID);
  
  /**
   * @return Participant|Membership|Contribution
   */
  function getLineItemTarget($int $lineItemID);

  function getPayments();
  
  function removeLineItem(int $lineItemID)
}

// Usage

$ci = new CiviInvoice();
$ci->addMembership(...membership1...);
$ci->addMembership(...membershp2...);
$ci->addContribution(...);
$entityManager->persist($ci);