The sync solution can use any store (file based, db based etc) as the sync metadata store if it can support harmoinca required metadata correctly and efficiently.
Currently the sync framework ships a SQL CE based metadata store component, though the idea of using other SQL Server store has been considered but it's not available at this moment.
The Microsoft.Synchronization.MetadataStorage assembly is a managed wrapper of metadata store compoment implemented in native COM, so ultimately it's still using SQLCE as the store. There is no way to work around this implementation.