A different reproducer is to use phc2sys to synchronize the system clock to a stable PTP hardware clock with a larger initial offset, which is not corrected by stepping to not reset the NTP error. This causes the frequency to be less stable and the measured offset to be larger than would be expected on the hardware.

For example:
# phc2sys -s /dev/ptp6 -m -O 0 -F 0.0
phc2sys[3445287.444]: phc offset 999954026 s0 freq  -16868 delay   1915
phc2sys[3445288.445]: phc offset 999954049 s2 freq  -16845 delay   1909
phc2sys[3445289.445]: phc offset 999954060 s2 freq +100000000 delay   1922
phc2sys[3445290.445]: phc offset 889018287 s2 freq +100000000 delay   1722
phc2sys[3445291.445]: phc offset 777881303 s2 freq +100000000 delay   1734
phc2sys[3445292.445]: phc offset 666744093 s2 freq +100000000 delay   1718
phc2sys[3445293.445]: phc offset 555610150 s2 freq +100000000 delay   1732
phc2sys[3445294.445]: phc offset 444473218 s2 freq +100000000 delay   1724
phc2sys[3445295.445]: phc offset 333336247 s2 freq +100000000 delay   1740
phc2sys[3445296.445]: phc offset 222199334 s2 freq +100000000 delay   1722
phc2sys[3445297.445]: phc offset 111062205 s2 freq +100000000 delay   1736
phc2sys[3445298.445]: phc offset    -74458 s2 freq  -91303 delay   1730
phc2sys[3445299.445]: phc offset    -43689 s2 freq  -82871 delay   1937
phc2sys[3445300.446]: phc offset     22285 s2 freq  -30004 delay   1913
...
phc2sys[3445372.454]: phc offset       -16 s2 freq  -16916 delay   1909
phc2sys[3445373.454]: phc offset       -38 s2 freq  -16942 delay   1925
phc2sys[3445374.454]: phc offset       -57 s2 freq  -16973 delay   1919
phc2sys[3445375.454]: phc offset       -85 s2 freq  -17018 delay   1926
phc2sys[3445376.454]: phc offset        83 s2 freq  -16875 delay   1921
phc2sys[3445377.454]: phc offset        50 s2 freq  -16884 delay   1929
phc2sys[3445378.454]: phc offset        54 s2 freq  -16865 delay   1911
phc2sys[3445379.454]: phc offset        26 s2 freq  -16876 delay   1936
phc2sys[3445380.454]: phc offset        14 s2 freq  -16881 delay   1911
phc2sys[3445381.455]: phc offset       -25 s2 freq  -16915 delay   1920
phc2sys[3445382.455]: phc offset       -41 s2 freq  -16939 delay   1920
phc2sys[3445383.455]: phc offset       -73 s2 freq  -16983 delay   1912

After restarting phc2sys with a small non-zero step threshold to force the step in order to reset the NTP error it settles down to smaller offsets:

# phc2sys -s /dev/ptp6 -m -O 0 -F 1e-9
phc2sys[3445424.661]: phc offset      -898 s0 freq  -16807 delay   1920
phc2sys[3445425.661]: phc offset     -1075 s1 freq  -16984 delay   1913
phc2sys[3445426.661]: phc offset       158 s2 freq  -16826 delay   1921
phc2sys[3445427.661]: phc offset       194 s2 freq  -16743 delay   1921
...
phc2sys[3445481.667]: phc offset         2 s2 freq  -16821 delay   1928
phc2sys[3445482.667]: phc offset        -1 s2 freq  -16824 delay   1923
phc2sys[3445483.667]: phc offset         6 s2 freq  -16817 delay   1912
phc2sys[3445484.668]: phc offset        -7 s2 freq  -16828 delay   1911
phc2sys[3445485.668]: phc offset         1 s2 freq  -16822 delay   1927
phc2sys[3445486.668]: phc offset        12 s2 freq  -16811 delay   1906
phc2sys[3445487.668]: phc offset        -1 s2 freq  -16821 delay   1934
phc2sys[3445488.668]: phc offset       -12 s2 freq  -16832 delay   1908
phc2sys[3445489.668]: phc offset        -4 s2 freq  -16827 delay   1901
phc2sys[3445490.668]: phc offset        -1 s2 freq  -16826 delay   1925
phc2sys[3445491.668]: phc offset         3 s2 freq  -16822 delay   1923
phc2sys[3445492.668]: phc offset        13 s2 freq  -16811 delay   1914

------- Comment From seg.com 2019-05-30 20:16 EDT-------
Not clear to me whether this is already fixed and we should close or not already fixed and we're not going to bother for RHEL 7, at a minimum.

We cannot fix this without bug #1131131, which was closed as WONTFIX. The nohz=off kernel option is recommended as a workaround for a highly accurate synchronization.