Tested with the simple fix and seems it fixed the issue and now persist-id tag is added to the confirmed commit:
2018-06-06 13:52:47,723 - ydk - DEBUG - Trace: Missing message-id in rpc.
2018-06-06 13:52:47,723 - ydk - DEBUG - Netconf SSH Client: sending rpc
2018-06-06 13:52:47,724 - ydk - DEBUG - Trace: Writing message (session 2711111191):

<?xml version="1.0"?>
<rpc xmlns="urn:ietf:params:xml:ns:netconf:base:1.0" message-id="5">
  <commit>
    <persist-id>1234</persist-id>
  </commit>
</rpc>

2018-06-06 13:52:47,724 - ydk - DEBUG - Netconf SSH Client: receiving rpc
2018-06-06 13:52:48,170 - ydk - DEBUG - Trace: Received message (session 2711

<rpc-reply message-id="5" xmlns="urn:ietf:params:xml:ns:netconf:base:1.0">
 <ok/>
</rpc-reply>

2018-06-06 13:52:48,170 - ydk - DEBUG - Netconf SSH Client: processing reply
2018-06-06 13:52:48,171 - ydk - INFO - =============Reply payload received fr
2018-06-06 13:52:48,171 - ydk - INFO -

<?xml version="1.0"?>
<rpc-reply xmlns="urn:ietf:params:xml:ns:netconf:base:1.0" message-id="5">
  <ok/>
</rpc-reply>