If I flash stock and unroot via Nexus Root Toolkit... will this turn off usb debugging?
Yes, the USB debugging would be found turned off.

The USB debugging settings are saved under /data, specifically mentioned under:


/data/property/persist.sys.usb.config
/data/data/com.android.settings/shared_prefs/com.android.settings_preferences.xml
/data/data/com.android.providers.settings/databases/settings.db


Because flashing a stock ROM would require you to wipe /data to avoid unforeseen issues, you would lose all the settings.

As you mentioned it yourself, flashing a custom ROM which has USB debugging turned on as default would be the best thing to do here. 

Note that if you're going to flash a ROM with Android 4.2.2 or above you would be required to authorize the debugging on Android. If you've a custom recovery, you may try my answer mentioned here and if you end up flashing a ROM with USB debugging turned off, this answer of mine may help.