Should sync script go in the root of bedrock project? project-root/site/scripts/ .
Do you mean the script that syncs the database + uploads/ files from one server to another?
I put that script into the project folder where also the wp-cli.yml and .env file is.
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While on the topic of the sync script, it would be awesome if this was configured to work with multisite networks. Any possible plans for that in the future?
Just set this up to work with our Multisite – it is possible 
Care to share more about how you set it up?