Currently, bigDiffy does not seem to support comparing natively partitioned BigQuery tables. I ran bigDiffy with $<partition>-decorated BQ tables on the rhs and lhs. The $partition argument was not retained in the arguments to the Dataflow job.
The job did not read any input records (according to the job graph) and failed after 15 minutes with NullPointerException messages (not 100% sure if the null pointers are related to the native partitioning).
FYI @catherinejelder