Cleanup of JSONSerializer and in place JSON coding calls in Serialization

We have a mix of two styles today since we were not sure how far we can push the Codable infra.

Perhaps we can completely remove `Serializer` types and replace them with "TopLevelEncoder" etc.

Start by mapping the Serialization area, including JSONSerializer, the Serializer types, and the in-place JSON coding calls mentioned in the issue. Compare the current mix of styles with Swift Codable's TopLevelEncoder APIs, then clarify whether removing Serializer types and adopting those APIs is the agreed scope before implementing or defining completion criteria.

Written by the indexing model from the issue text.