docker: use 3.0 way to startup in readme

It is recommended for modern Tarantool based applications to use a
startup flow with `config.yaml` instead of starting of a Lua script.

Adjusted container/application/instance names to be consistent across
examples.

* container: `app-instance-001`
* application: `app`
* instance: `instance-001`

NO_DOC=it is a documentation change itself
NO_CHANGELOG=no code is changed
NO_TEST=see NO_CHANGELOG