Modernizing your Classic SharePoint sites is an optional step you can do before or after accomplishing the steps in ShortPoint Microsoft 365 Classic Pages Deprecation: Transforming Classic Pages to Modern Pages. To learn how to modernize your Classic SharePoint sites, you can check out the solutions provided in Modernize your classic SharePoint sites.
This step is only required to make Theme Builder work on System pages. It is not required for designing pages in SharePoint. Take note that the solutions in the article are provided by Microsoft 365. Thus, ShortPoint's Support may not be able to assist with the solutions mentioned in the article.