My org has a very large AWS spend and we got to have a chat with some of their SWE's that work on the geospatial processing features for Redshift and Athena. We described what we needed and they said our only option was to aggregate the data first or drop the offending rows. Obviously we're not interested in compromising our work just to use a specific tool, so we opted for better tools.
The crux of the issue was that the large problem column was the geometry itself. Specifically, MultiPolygon. You need to use the geometry datatype for this[1]. However, our MultiPolygon column was 10's to 100's of MB's. Well outside the max size for the Super datatype from what I can tell as it looks like that's 16 MB.
[1]: https://docs.aws.amazon.com/redshift/latest/dg/GeometryType-...