When restoring a Google Drive folder to a previous version, will the restore overwrite the latest version?

Definitely NOT.

Safe restore

By default, all restored data will be placed into a separate folder named Restored<date-time>, in order to distinguish it from the original data. If you choose to restore the data to a specific folder (even the original folder!), CubeBackup will not overwrite any files in that location. The folder will simply contain multiple files with identical names. You can distinguish the files by date created.

More information about the data restore is available at Restore Google Drive files or folders.