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Hi,
I believe the setting you want is SyncOptionIgnoreDataCompression (True by default), documented here:
https://documentation.red-gate.com/sca/developing-databases/concepts/advanced-concepts/comparison-and-script-generation-options
You can set this before baselining in Visual Studio (by opening up the settings file on disk before completing the setup wizard), but not yet in SSMS.
You can set it after baselining in both.
The ability to set this before baselining in SSMS via the UI will likely be released this week.
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Eric