I do not know of anyway to make the plugin reliably spin down the drives - this is something Unraid still struggles to do reliably for all hardware combinations so it something I have been avoiding. At the moment if you want spindown then you need it set appropriately at the Unraid system level. The plugin does, however, now avoid unnecessarily spinning up drives if a check is in a paused state for temperature related reasons.
Having said that I will consider checking if the latest Unraid releases have cracked the problem of spindown in a way the plugin can exploit. It might be worth attempting a spindown when the temperature related pause happens even if it does not work for everybody. If I get this working it will probably have to be exposed as a setting as I could see that not everyone would want their drives forcibly spun down by the plugin.