Consolidate all caller of io_ops_commit() to call td_io_commit()

[dennischerchang]

Calling io_ops->commit() will not update io_u_in_flight and io_u_queued accordingly. If iio_u_queued is not reset properly the fio may need to make unnecessary stop to drain the queue. Which may degrade the throughput.

Fix issue: #2052

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Reminders:

1. If you modify struct thread_options, also make corresponding changes in
   cconv.c and bump FIO_SERVER_VER in server.h
2. If you change the ioengine interface (hooks, flags, etc), remember to bump
   FIO_IOOPS_VERSION in ioengines.h.