I'm sorry, but it seems there was a misunderstanding about the report, that you are using. Are you using the Community app "Cycle Time Report"? That report doesn't have the option to exclude non-workdays.
Apps from the Community have been carefully selected and reviewed by our engineering team. While these apps will now be much easier for customers to add to their custom pages, we will provided limited support for them and they are subject to beta terms. Please see also Product Announcement - New App Catalog with Community Apps
Anny issues with and/or changes to these apps: you are encouraged to open an issue in GitHub (links to GitHub repos are provided with each community app in the app catalog) or to correct the issue yourself and create a pull request for it.