Temp tables are not visibile outside of a single connection, so the autovacuum worker connection isn't able to see it.
I can connect as a superuser via psql while temp tables are being used and I can examine tables in the pg_temp_* schemas, so that particular separation isn't really a strong one. If there's a reason why autovacuum isn't doable on temp tables, it's not that one. (maybe autovacuum would work on the tables while the session disconnects, preventing the temp tables from being dropped?)
