Why is SQLAlchemy count() much slower than the raw query?

Unfortunately MySQL has terrible, terrible support of subqueries and this is affecting us in a very negative way. The SQLAlchemy docs point out that the “optimized” query can be achieved using query(func.count(Segment.id)):

Return a count of rows this Query would return.

This generates the SQL for this Query as follows:

SELECT count(1) AS count_1 FROM (
     SELECT <rest of query follows...> ) AS anon_1

For fine grained control over specific columns to count, to skip the
usage of a subquery or otherwise control of the FROM clause, or to use
other aggregate functions, use func expressions in conjunction with
query(), i.e.:

from sqlalchemy import func

# count User records, without
# using a subquery.
session.query(func.count(User.id))

# return count of user "id" grouped
# by "name"
session.query(func.count(User.id)).\
        group_by(User.name)

from sqlalchemy import distinct

# count distinct "name" values
session.query(func.count(distinct(User.name)))