Hello,
There's no option to avoid transforming specific content types, only section tags can be omited.
You can remove contents such as comments from the main body using DOCXPath (https://www.phpdocx.com/api-documentation/docx-path/remove-elements-in-docx) before transforming the content.
We have moved the request to dev team to add support in the next release of phpdocx.
Regards.