my-db.dig

_export:
  host: 'localhost'
  user: 'me'
  password: 'my-pass'
  database: 'my-database'
  project_id: 'my-projectid'
  dataset: 'my-dataset'

my.dig

timezone: UTC

schedule:
  daily>: 10:00:00

+main:
  !include : my-db.dig

  +step1:
    for_each>:
      table: [
        users
        , products
      ]
    _do:
      embulk>: mysql_to_bigquery.yml

  +step2:
    embulk>: mysql_to_bigquery_orders.yml

mysql_to_bigquery.yml

in:
  type: mysql
  host: ${host}
  user: ${user}
  password: '${password}'
  database: ${database}
  table: ${table}
out:
  type: bigquery
  mode: replace
  auth_method: json_key
  json_keyfile: ./my-bigquery.json
  project: ${project_id}
  dataset: ${dataset}
  auto_create_table: true
  table: ${table}
  allow_quoted_newlines: true

mysql_to_bigquery_orders.yml

in:
  type: mysql
  host: ${host}
  user: ${user}
  password: '${password}'
  database: ${database}
  query: |
    select id,user_id,product_id from orders
out:
  type: bigquery
  mode: replace
  auth_method: json_key
  json_keyfile: ./my-bigquery.json
  project: ${project_id}
  dataset: ${dataset}
  auto_create_table: true
  table: orders
  allow_quoted_newlines: true

ブログ拝見しました。
Digdagクライアントでもシークレット使えるはずですが
これじゃダメですか？
http://docs.digdag.io/command_reference.html#secrets

追記
もしかして、ローカルモードではなく、スケジューラでシークレットが使えないと言う話ですか？