[Chore] Unify APIs around letting data be filtered

[emkornfield]

Please describe why this is necessary.

We migrated write_json_files to take FilteredEngineData instead of EngineData because it will be used to support remove actions by passing back scan FilterBatches into the API.

this was a tactical change but we should likely be consistent with Engine APIs to take FilteredEnginedata or collapse the concept of FilteredEngineData and EngineData so that all batches end up being filtered. This should probably have a little bit more design to come to a final solution.

Describe the functionality you are proposing.

No response

Additional context

Creating issue based on Review request

[emkornfield]

CC @zachschuermann