The Advisor packs have commercial url's encoded by default. To point them to Azure Gov or any other Azure installation you will have to use overrides in SCOM.
The advisor rules are targetting the healthservice for the most part. The easiest way is to override all rules to point to your desired Azure. The achieve this open authoring and change the scope to select healthservice.
I prefer targetting the "Microsoft System Center Advisor Monitoring Server Group" because this gives more control on the agents that you want connected to your Azure via the Log analytics management pack.
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