Hello,
UPDATE: phpdocx 12 added support to images embedded in shapes when using merge methods.
Images embedded in shapes aren't supported in the current stable release of the merging class, only normal images are supported. Merging shapes is supported but not when they have an embedded image.
On the API documentation page of the method (https://www.phpdocx.com/api-documentation/docxutilities/merge-Word-documents-with-PHP) you can read the supported contents when merging the documents with mergeDocx in the current stable version. As you can read, all contents without internal/external dependencies are supported (paragraphs, tables, run-of-text, bookmarks, text boxes, fields...) and also the following contents with internal dependencies: styles, images, charts, links, cross-references, lists, altChunks, footnotes, endnotes, comments, headers, footers and sections; shapes aren't listed as supported contents when merging with dependencies, although they are supported if they don't have an internal/external dependency such as an image.
The testing branch includes support for embedded images in shapes that will be included in the next release of phpdocx (there's no release date). Advanced and Premium licenses with LUS active (https://www.phpdocx.com/updates) can get features available in the testing branch but not in the stable version; if your license includes an active LUS please send an email to contact[at]phpdocx.com with the following information: you are using the classic or namespaces package, and the dev team will send you the updated class.
Regards.