Clean up `.model.transport` after migration

As suggested by @glatterf42 in his review of #207:

- [1](https://github.com/iiasa/message-ix-models/pull/207#discussion_r1699623381): in doc/transport/input.rst, a reference to message_data.model.transport.
- Expand type hints ([2](https://github.com/iiasa/message-ix-models/pull/207#discussion_r1699649767), [3](https://github.com/iiasa/message-ix-models/pull/207#discussion_r1699653863))