Normally (under Windows) SMB v3 supports the real-time watching for changed files. ATM this function seems to be broken on QTS (maybe it doesn’t work on Linux in general or suffers from settings in QNAP’s Linux/SAMBA implementation you can’t change, I really don’t know). Other users also reported that the HD’s on the NAS never go to sleep when using Roon setups similar to yours. What you can try is:
Login to your QNAP, open up the Control Panel and navigate to the settings page for Win/Mac/NFS in the Network & File Services section. Click on Advanced Options and change the setting for Highest SMB Version: to SMB 2.1 (default is SMB 3.0).
To make sure the setting gets applied you should restart the NAS afterwards. You should also restart your Roon Core. The Automatic Rescan Interval setting should now show up for your storage.