FdoDataType_UniqueID appears to be a GUID logical data type in FDO that whose implementation appears to be either in draft or in limbo (possibly explaining why all such references to this enum value are commented out and there's no mention of this data type in the public API)
A shame, because I'd like FDO to support GUIDs at the API level.
But to answer your question specifically. If you're inserting a feature into a feature class that has an auto-generated property a value should be generated for you, so when preparing a FDO insert command, you simply omit setting a value for the auto-generated property.
You can inspect this new value as part of the feature reader that's returned by FdoIInsert::Execute()