Running from subfolder isn’t an option when using a CSV. It is only for non-CSV batches. In the SPA user interface, when you select the CSV checkbox, you will see the use subfolder checkbox become disabled too so it isn’t even available.
I tried to make subfolders run when using a CSV. However, there were several complication in doing that in the plugin API and I couldn’t get it to work. Therefore, the option is disabled when running from a CSV.