When I was analyzing the results of my little 2-server 2-client testing, I started wondering why the chronyd server's accuracy was not as good as I expected when syncing to the GPS NTP Appliance TM1000A. I found the
"presend" option for a server declaration, which reads in part:

If the timing measurements being made by chronyd are the only network
data passing between two computers, you might find that some
measurements are badly skewed due to either the client or the server
having to do an ARP lookup on the other party prior to transmitting a
packet. This is more of a problem with long sampling intervals, which
might be similar in duration to the lifetime of entries in the ARP
caches of the machines.

Local LAN:  check.
Long sample times:  check.
Only network traffic between the server and appliance:  check.

For the local appliance setting in my firewall, I set up this server line:

server 10.1.2.15 minpoll 4 maxpoll 6 iburst prefer presend 4

* 10.1.2.x is the separate VLAN I set up for the appliance, so that the embedded TCP/IP stack sees a minimum of traffic.
* Set the minimum polling time to 16 seconds (default is 64)
* Set the maximum polling time to 64 seconds (default is 1024)
* Use iburst to obtain a useful set of measurements at startup
* Prefer the local appliance when it is available
* Use presend to exchange a packet (and set up ARP in both devices) before taking a measurement.

Note that this should be done ONLY for a locally-connected NTP stratum 1 server, and not with public servers.

The resulting information, after making the above change:
chronyc> ntpdata 10.1.2.15 (edited for brevity)
Leap status     : Normal
Version         : 4
Mode            : Server
Stratum         : 1
Poll interval   : 6 (64 seconds)
Precision       : -10 (0.000976562 seconds)
Root delay      : 0.000000 seconds
Root dispersion : 0.000000 seconds
Reference ID    : 47505300 (GPS)
Reference time  : Sun May 13 02:00:22 2018
Offset          : +0.000211241 seconds
Peer delay      : 0.000976595 seconds
Peer dispersion : 0.000976596 seconds
Response time   : 0.000000000 seconds
Jitter asymmetry: +0.00
NTP tests       : 111 111 1111

chronyc> tracking                 (edited for brevity)
Stratum         : 2
System time     : 0.000073854 seconds fast of NTP time
Last offset     : +0.000098993 seconds
RMS offset      : 0.000139127 seconds
Frequency       : 11.131 ppm slow
Residual freq   : +0.023 ppm
Skew            : 0.615 ppm
Root delay      : 0.000976595 seconds
Root dispersion : 0.000997213 seconds
Update interval : 64.2 seconds
Leap status     : Normal



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