If you have added the Joomla button to the editor toolbar, then the buttons are included in a drop-down menu from that button, not below the editor, eg:

The Yootheme Pro button is missing in the dropdown.

Which Yootheme Pro button are you referring to? I don't see it in the screenshot of your original post.

It would be great if there is a way to place buttons again below the editor. Users who use Yootheme are used to it and can not find it anymore (which leads to increased support requests). It also needs a lot more clicks now.

Remove the Joomla button from the editor toolbar in Editor Profiles -> Features & Layout.

Only buttons that are installed as editor-xtd buttons can be included in the Joomla drop-down menu. The Yootheme Builder button appears to be added dynamically in a seperate process, so it is not available to be included in the menu.

Please try JCE Pro 2.8.2 Beta1 - https://www.joomlacontenteditor.net/downloads/editor/pro/development - which makes allowance for this so that the Yootheme Builder button is still able to be rendered at the bottom of the editor, if the Joomla menu is added to the editor toolbar.