Absolutely! Each SQL instance (and even database) can have its own unique thresholds in AppInsight for SQL. When viewing the Application Details of the SQL instance you wish to modify the threshold for, simply click the "Edit Application Monitor" link in the top right.
Image may be NSFW.
Clik here to view.
From there you will be taken to the application editor for that SQL instance on that node. Any thresholds or settings defined here will be unique to this specific SQL instance.
