Sorry, didn't see it before.
So I had it wrong when testing and used a regular object type rather than nested.
I do think there's currently no way to use nested field types with runtime field.
Based on this answer it seems that deprecated scripted field can provide some help manually accessing the nested structure via _source, but that will have some performance impact: ElasticSearch aggregate on a scripted nested field - #2 by doogyatnesta