In !25230 (merged), the OR "milestones"."group_id" IN (...) part is now:

WITH RECURSIVE "base_and_ancestors" AS
  (SELECT "namespaces".*
   FROM
     (SELECT "namespaces".*
      FROM "namespaces"
      INNER JOIN "members" ON "namespaces"."id" = "members"."source_id"
      WHERE "members"."source_type" = 'Namespace'
        AND "namespaces"."type" IN ('Group')
        AND "members"."user_id" = 3245056
        AND "members"."type" IN ('GroupMember')
        AND "members"."requested_at" IS NULL
      UNION SELECT namespaces.*
      FROM "projects"
      INNER JOIN "namespaces" ON "namespaces"."id" = "projects"."namespace_id"
      INNER JOIN "project_authorizations" ON "projects"."id" = "project_authorizations"."project_id"
      WHERE "project_authorizations"."user_id" = 3245056) namespaces
   WHERE "namespaces"."type" IN ('Group')
   UNION SELECT "namespaces".*
   FROM "namespaces",
        "base_and_ancestors"
   WHERE "namespaces"."type" IN ('Group')
     AND "namespaces"."id" = "base_and_ancestors"."parent_id"),
               "base_and_descendants" AS
  (SELECT "namespaces".*
   FROM "namespaces"
   INNER JOIN "members" ON "namespaces"."id" = "members"."source_id"
   WHERE "members"."source_type" = 'Namespace'
     AND "namespaces"."type" IN ('Group')
     AND "members"."user_id" = 3245056
     AND "members"."type" IN ('GroupMember')
     AND "members"."requested_at" IS NULL
   UNION SELECT "namespaces".*
   FROM "namespaces",
        "base_and_descendants"
   WHERE "namespaces"."type" IN ('Group')
     AND "namespaces"."parent_id" = "base_and_descendants"."id")
SELECT "id"
FROM
  (SELECT "namespaces".*
   FROM "base_and_ancestors" AS "namespaces"
   WHERE "namespaces"."type" IN ('Group')
   UNION SELECT "namespaces".*
   FROM "base_and_descendants" AS "namespaces"
   WHERE "namespaces"."type" IN ('Group')) namespaces
WHERE "namespaces"."type" IN ('Group')
ORDER BY "namespaces"."id" DESC)

SELECT
    COUNT(*) AS count_all,
    "milestones"."state" AS milestones_state
FROM
    "milestones"
WHERE ("milestones"."project_id" IN (
        SELECT
            "projects"."id"
        FROM
            "projects"
            INNER JOIN "project_authorizations" ON "projects"."id" = "project_authorizations"."project_id"
        WHERE
            "project_authorizations"."user_id" = 3245056
            AND "projects"."archived" = 'f'
        ORDER BY
            GREATEST (COALESCE(last_activity_at, '1970-01-01'),
                COALESCE(last_repository_updated_at, '1970-01-01'))
            DESC)
        OR "milestones"."group_id" IN (


          WITH RECURSIVE "base_and_ancestors" AS
            (SELECT "namespaces".*
             FROM
               (SELECT "namespaces".*
                FROM "namespaces"
                INNER JOIN "members" ON "namespaces"."id" = "members"."source_id"
                WHERE "members"."source_type" = 'Namespace'
                  AND "namespaces"."type" IN ('Group')
                  AND "members"."user_id" = 3245056
                  AND "members"."type" IN ('GroupMember')
                  AND "members"."requested_at" IS NULL
                UNION SELECT namespaces.*
                FROM "projects"
                INNER JOIN "namespaces" ON "namespaces"."id" = "projects"."namespace_id"
                INNER JOIN "project_authorizations" ON "projects"."id" = "project_authorizations"."project_id"
                WHERE "project_authorizations"."user_id" = 3245056) namespaces
             WHERE "namespaces"."type" IN ('Group')
             UNION SELECT "namespaces".*
             FROM "namespaces",
                  "base_and_ancestors"
             WHERE "namespaces"."type" IN ('Group')
               AND "namespaces"."id" = "base_and_ancestors"."parent_id"),
                         "base_and_descendants" AS
            (SELECT "namespaces".*
             FROM "namespaces"
             INNER JOIN "members" ON "namespaces"."id" = "members"."source_id"
             WHERE "members"."source_type" = 'Namespace'
               AND "namespaces"."type" IN ('Group')
               AND "members"."user_id" = 3245056
               AND "members"."type" IN ('GroupMember')
               AND "members"."requested_at" IS NULL
             UNION SELECT "namespaces".*
             FROM "namespaces",
                  "base_and_descendants"
             WHERE "namespaces"."type" IN ('Group')
               AND "namespaces"."parent_id" = "base_and_descendants"."id")
          SELECT "id"
          FROM
            (SELECT "namespaces".*
             FROM "base_and_ancestors" AS "namespaces"
             WHERE "namespaces"."type" IN ('Group')
             UNION SELECT "namespaces".*
             FROM "base_and_descendants" AS "namespaces"
             WHERE "namespaces"."type" IN ('Group')) namespaces
          WHERE "namespaces"."type" IN ('Group')
          ORDER BY "namespaces"."id" DESC


        )
)
GROUP BY
    "milestones"."state"

☝ the new version, full query. Analysis/discussion: https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/25230#note_142154333