Here's a way to disable automatic scanning of folders. Unfortunately, I cannot check it since being away from home studio. Could someone please check and confirm if it works?
Sure, it is possible to set this up in XO with a system file, you can add that to your user folder for XO.
Create a text file called:
disable_startupsync.txt
And place it in your user folder for XO:
Documents\XO\xxxxxx\Settings\
*xxxxxx = folder with numbers specific to the user
Please give this a try and see if you can get the automatic startup scanning to be disabled, let me know if this works for you.