a.py

from sqlalchemy import Table, Column, Integer, String, MetaData, ForeignKey
from sqlalchemy.orm import sessionmaker

Session = sessionmaker()
session = Session()

metadata = MetaData()
table1 = Table('table1', metadata,
    Column('id', Integer, primary_key=True),
    Column('name', String),
)

table2 = Table('table2', metadata,
    Column('id', Integer, primary_key=True),
    Column('table1_id', None, ForeignKey('table1.id')),
)

table3 = Table('table3', metadata,
    Column('id', Integer, primary_key=True),
    Column('table2_id', None, ForeignKey('table2.id')),
)

from sqlalchemy.sql import select
print select(
        [table1, table2, table3]
    ).select_from(
        table1.join(
            table2.join(table3)
        )
    )

print "----"

t = session.query(table1).limit(100).subquery('T1')
print select(
        [t, table2, table3]
    ).select_from(
        t.join(
            table2.join(table3)
        )
    )

"""

$ python a.py
SELECT table1.id, table1.name, table2.id, table2.table1_id, table3.id, table3.table2_id
FROM table1 JOIN (table2 JOIN table3 ON table2.id = table3.table2_id) ON table1.id = table2.table1_id
----
SELECT "T1".id, "T1".name, table2.id, table2.table1_id, table3.id, table3.table2_id
FROM (SELECT table1.id AS id, table1.name AS name
FROM table1
 LIMIT :param_1) AS "T1" JOIN (table2 JOIN table3 ON table2.id = table3.table2_id) ON "T1".id = table2.table1_id

"""