There was no option per say, at least on the ubuntu installed I tried many years ago. Just a popup that happened sometime before the install but after the manual partitioning if the root partition had folders like /etc /usr /var etc that were needed by the installer. Not sure if all installers do this - but I would suspect if they didnt you can just delete the folders manually before you enter the installer and pick manual partitioning option and opt to not format any partitions.