glibcs malloc is not obstack, its not a simple linear heap where one object on top means everything below is not freeable. It also uses MADV_DONTNEED give sbrk'd memory back to the system. This is the place where MADV_FREE can now be used now as the latter does not guarantee a page fault.
But that said of course you can construct workloads which lead to increased memory usage also with malloc and maybe python triggers them more often than other applications. Is there an existing issues showing the problem? It would be a good form of documentation in the source.