Hello,
Your statement about federated queries not supporting Cloud SQL Server is correct as the documentation states that it only supports MySQL 2nd generation and PostgreSQL instances.
If you refer to this StackOverflow post, the accepted answer mentions using some third party products to connect your Cloud SQL Server instance to BigQuery, or make use of Cloud Dataflow. The suggestions made there might interest you.
If you are specifically interested in using federated queries, then you may also open a Feature Request asking for federated queries to support Cloud SQL Server by following the instructions here; I currently do not see any requests of that nature yet, so opening a request may push the addition of that feature forward.
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