Thanks, I misunderstood the question. I understood nested as in "nested object" but not "nested data type".
Aggregations on nested fields require the nested aggregation, so this is not a transform limitation, but a limitation in the aggregation framework. Transform is using composite aggregations, which does not support this case.
I doubt that we add support for it, because this has scalability issues. Un-nesting is limited but composite aggregations and transform are meant for bigger data sets.
Maybe you can change you input data layout or if the data is small just use an ordinary aggregation instead of a transform.