Hello,
linebreak is not supported, so we recommend you to use the API of phpdocx to add MS Word breaks or split the equation into multiple math elements.
You can change the output of the document using DOCXPath (https://www.phpdocx.com/documentation/introduction/docxpath) to remove contents (for example that empty input you refer), inserting new elements (for example adding breaks instead of using the linebreak tag), moving elements and cloning contents.
DOCXPath is available in Advanced and Premium licenses. After you have purchased an Advanced or Premium license please contact us again and we'll create a script to show you how to accomplish both tasks.
Regards.