Ikke helt sikker på hvorfor, men det ser ud til at virke, når du først opretter en forbindelse og kører COMMIT :
In [8]: conn = engine.connect()
In [9]: conn.execute("COMMENT ON SCHEMA myschema IS 'Seemly Random Description'")
Out[9]: <sqlalchemy.engine.result.ResultProxy at 0x7fd109991cd0>
In [10]: conn.execute("COMMIT;")
Out[10]: <sqlalchemy.engine.result.ResultProxy at 0x7fd0ff3b7d10>
postgres=# \dn+
List of schemas
Name | Owner | Access privileges | Description
----------+----------+----------------------+---------------------------
myschema | postgres | | Seemly Random Description
public | postgres | postgres=UC/postgres+| standard public schema
| | =UC/postgres |