From the Schema Compare Options, I deselected all Object Types:
It still shows me differences in Schema objects:
I scrolled through the big list of General options, and none of them appeared to do this:
I hacked it. If you save the compare, you can add this to the file:
<PropertyElementName>
<Name>Microsoft.Data.Tools.Schema.Sql.SchemaModel.SqlSchema</Name>
<Value>ExcludedType</Value>
</PropertyElementName>
You'll see where when you open it. This setting is not in the UI, but is apparently supported.
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