main: don't break graceful shutdown on init script exit

Graceful shutdown is done in a special fiber which is started for
example on SIGTERM. So it can run concurrently with fiber executing
Tarantool init script. On init fiber exit we break event loop to pass
control back to the Tarantool initialization code. But we fail to run
event loop a bit more to finish graceful shutdown.

The test is a bit contrived. A more real world case is when Tarantool is
termintated during lingering box.cfg().

Close #9411

NO_DOC=bugfix