starting chronyd                                      	OK
  running chronyc dfreq 1e-3                            	OK
  checking chronyc output                               	OK
    DATE 1 1585758870
  running chronyc doffset -30.0                         	OK
    DATE 2 1585758870
  checking chronyc output                               	OK
    DATE 3 1585758870
  running chronyc makestep                              	OK
    DATE 4 1585758870
  checking chronyc output                               	OK
    DATE 5 1585758870
    DATE S1 1585758870
    DATE SET Wed Apr  1 16:34:35 UTC 2020
    DATE S2 1585758870
    DEBUG before 1585758870
    DEBUG after 1585758870
    DEBUG S1: * chrony.service - chrony, an NTP client/server
     Loaded: loaded (/lib/systemd/system/chrony.service; enabled; vendor preset: enabled)
     Active: active (running) since Wed 2020-04-01 16:34:25 UTC; 4s ago
       Docs: man:chronyd(8)
             man:chronyc(1)
             man:chrony.conf(5)
   Main PID: 5499 (chronyd)
      Tasks: 2 (limit: 1660)
     Memory: 5.9M
     CGroup: /system.slice/chrony.service
             |-5499 /usr/sbin/chronyd -F -1
             `-5500 /usr/sbin/chronyd -F -1

Apr 01 16:34:25 autopkgtest systemd[1]: Starting chrony, an NTP client/server...
Apr 01 16:34:25 autopkgtest chronyd[5499]: chronyd version 3.5 starting (+CMDMON +NTP +REFCLOCK +RTC +PRIVDROP +SCFILTER +SIGND +ASYNCDNS +SECHASH +IPV6 -DEBUG)
Apr 01 16:34:25 autopkgtest chronyd[5499]: Loaded seccomp filter
Apr 01 16:34:25 autopkgtest systemd[1]: Started chrony, an NTP client/server.
    DEBUG S2: * systemd-timesyncd.service - Network Time Synchronization
     Loaded: loaded (/lib/systemd/system/systemd-timesyncd.service; enabled; vendor preset: enabled)
    Drop-In: /usr/lib/systemd/system/systemd-timesyncd.service.d
             `-disable-with-time-daemon.conf
     Active: active (running) since Wed 2020-04-01 16:33:44 UTC; 45s ago
       Docs: man:systemd-timesyncd.service(8)
   Main PID: 602 (systemd-timesyn)
     Status: "Initial synchronization to time server 91.189.91.157:123 (ntp.ubuntu.com)."
      Tasks: 2 (limit: 1660)
     Memory: 8.0M
     CGroup: /system.slice/systemd-timesyncd.service
             `-602 /lib/systemd/systemd-timesyncd

Apr 01 16:33:43 autopkgtest systemd[1]: Starting Network Time Synchronization...
Apr 01 16:33:44 autopkgtest systemd[1]: Started Network Time Synchronization.
Apr 01 16:33:45 autopkgtest systemd-timesyncd[602]: Initial synchronization to time server 91.189.91.157:123 (ntp.ubuntu.com).
    DEBUG O1: 
    DEBUG O2: 
    DEBUG P1: 0     0    6057    6055  20   0   5056  1792 pipe_w S    ?          0:00                                          \_ grep chronyd
5   111    5499       1  20   0  15104  4160 do_sel S    ?          0:00 /usr/sbin/chronyd -F -1
1   111    5500    5499  20   0   7104  4224 skb_wa S    ?          0:00  \_ /usr/sbin/chronyd -F -1
5     0    6028       1  20   0   6656  4160 do_sel S    ?          0:00 ../../chronyd -l /tmp/autopkgtest.ChF59G/build.rot/src/test/system/tmp/chronyd.log -f /tmp/autopkgtest.ChF59G/build.rot/src/test/system/tmp/chronyd.conf -u root
  checking system clock                                 	BAD

That means systemd-timesyncd + chronyd from the package fight with the test's chrony.
This needs to be fixed in the test setup (and understood how it happened to have both runnng).