net: lwm2m: Fix separate response handling

Separate response handling implemented in the engine was faulty. The
separate response was not acknowledged by the client, resulting in
spurious retransmissions from the server side.

Also, the pending CON message was retransmitted by the client even after
it was acknowledged by an empty ACK, but the respnse haven't arrived
yet. Fix this by adding a new `acknowledged` flag to the `lwm2m_message`
structure. Once acknowledged, the flag is set and the confirmable
message is no longer retransmitted. We keep the message on the pending
list in order to timeout properly in case separate response does not
arrive in time.

Finally, prevent the reply callback from being called twice in case
the response is transmitted separately from ACk. The callback should
only be called on the actual reply, not the empty ACK.

Signed-off-by: Robert Lubos <robert.lubos@nordicsemi.no>