phpdocx can overwrite all styles, but the type to be customized may change depending on the style. For example, a font size or a font family can be applied as global style (setDefaultFont or setDocumentDefaultStyles methods), as a custom paragraph/character style (DocxCustomizer/sample_9.php example), as a paragraph style (DocxCustomizer/sample_1.php example) or as a run style (DocxCustomizer/sample_8.php example).
If some style is not being changed is because the correct target/type (https://www.phpdocx.com/api-documentation/docxcustomizer/customize-docx-Word-documents-PHP target and type options) are not being selected.
Please check the samples included in examples/DocxCustomizer. If you post the code you are using to change the styles we'll check it.