This server doc should help a bit - ArcGIS REST API - Services and Data Types
per replica (geodatabase) means that individual layers cannot sync independently and per layer means that they can be. With that, the table at the bottom shows that versioned data is per replica and non versioned is per layer.
If you use Enums.SyncModelGeodatabase in your generate parameters, then use SyncGeodatabaseParameters::geodatabaseSyncDirection property. Otherwise, if you used Enums.SyncModelLayer, use the layerOptions property.
SyncGeodatabaseParameters QML Type | ArcGIS for Developers
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