`tarantoolctl start` patches box.cfg two times:
1) before the init script to set default values and enforce some others,
2) after the init script to prevent changing a pid_file in runtime.

The second patching fails if an init file does not call
box.cfg{} before it's finished. This can take a place in apps with
managed instances which receive configuration from external server.

This patch moves the second patching into the box.cfg
wrapper created during the first patching. So the second patching
is performed only after box.cfg{} was invoked, so it does not fail anymore.

However there is relatively minor flaw for applications that
invoke box.cfg{} after init script is finished:
`tarantoolctl start` goes to background only when box.cfg{} is called.
Though this is not the case for daemon management systems like systemd,
as they handle backgrounding on their side

Fixes #4435

@TarantoolBot document
Title: tarantoolctl allows to start instances without a box.cfg{}

tarantoolctl now works for instances without box.cfg{} or
with delayed box.cfg{} call. This can be managed instances which receive
configuration from external server.

For such instances `tarantoolctl start` goes to background when
box.cfg{} is called, so it will wait until options for box.cfg are received.
However this is not the case for daemon management systems like systemd,
as they handle backgrounding on their side.