The new manager faces several disadvantages. For example, he won't be able to sign the players he wants because the transfer window has closed. He will also aim to be a tough opponent for Bayern Munich in Germany. Knowing that expectations are high, he will strive to succeed with a squad he didn't build. The new manager will have a truly significant responsibility. Appointing the Dutch manager from the start was a complete mistake. I'm sure the management has realized this by now. This mistake could cause problems for Bayer Leverkusen until the winter transfer window.
Your points are good and highlight significant challenges facing new manager. It is clear that manager who has been widely reported to be Erik ten Hag is at disadvantage because he can not bring in his own players due to transfer window closed. This is huge problem. He has been given team he did not build and as you noted team that has lost several key players from their championship winning season. This puts immense pressure on him to get results with squad that is very different from one that had so much success. Your feeling that club management made mistake with their first choice is also correct as they realized it was not working and made change very quickly. As you said this instability and poor performance will likely be problem for club until next transfer window opens.