I was able to override it using /etc/systemd/system/apt-
daily.timer.d/override.conf with this config:

###

[Timer]
OnCalendar=
OnCalendar=*-*-* 02:00
RandomizedDelaySec=4h
AccuracySec=1m
Persistent=true

###

Which Means:

        OnCalendar | Any day *-*-* at 02:00hrs. NOTE: See the first empty 
OnCalendar, this was needed otherwise the time defined in here was added from 
the previous schedule instead of replaced. 
(https://github.com/systemd/systemd/issues/3233)
RandomizedDelaySec | Add a random delay of up to 4:00hrs [02:00-06:00]
       AccuracySec | Start the process at any time within 1m of the calculated 
time (oncalendar + randomizeddleaysec) this results in [02:00-06:01]

---

Default is:

###

[Timer]
OnCalendar=*-*-* 6,18:00
RandomizedDelaySec=12h
AccuracySec=1h

###

Which means:
        OnCalendar | Any day *-*-* at 06:00hrs and 18:00hrs
RandomizedDelaySec | Add a random delay of up to 12:00hrs [06:00-18:00, 
18:00-06:00] (NOTE: at this point it could be any time!)
       AccuracySec | Start the process at any time within 1h of the calculated 
time (oncalendar + randomizeddleaysec) this results in [06:00-19:00, 
18:00-07:00]


---

Here I tested the overridden configuration:

# systemctl list-timers | grep -P "NEXT|apt"
NEXT                         LEFT     LAST                         PASSED       
UNIT                         ACTIVATES
Fri 2017-04-21 05:46:11 CDT  17h left Thu 2017-04-20 11:42:55 CDT  3min 29s ago 
apt-daily.timer              apt-daily.service
# systemctl restart apt-daily.timer && systemctl list-timers | grep -P 
"NEXT|apt"
NEXT                         LEFT     LAST                         PASSED       
UNIT                         ACTIVATES
Fri 2017-04-21 02:58:14 CDT  15h left Thu 2017-04-20 11:42:55 CDT  3min 44s ago 
apt-daily.timer              apt-daily.service
# systemctl restart apt-daily.timer && systemctl list-timers | grep -P 
"NEXT|apt"
NEXT                         LEFT     LAST                         PASSED       
UNIT                         ACTIVATES
Fri 2017-04-21 04:05:12 CDT  16h left Thu 2017-04-20 11:42:55 CDT  3min 53s ago 
apt-daily.timer              apt-daily.service
# systemctl restart apt-daily.timer && systemctl list-timers | grep -P 
"NEXT|apt"
NEXT                         LEFT     LAST                         PASSED      
UNIT                         ACTIVATES
Fri 2017-04-21 05:44:41 CDT  17h left Thu 2017-04-20 11:42:55 CDT  4min 0s ago 
apt-daily.timer              apt-daily.service
# systemctl restart apt-daily.timer && systemctl list-timers | grep -P 
"NEXT|apt"
NEXT                         LEFT     LAST                         PASSED      
UNIT                         ACTIVATES
Fri 2017-04-21 03:05:18 CDT  15h left Thu 2017-04-20 11:42:55 CDT  4min 1s ago 
apt-daily.timer              apt-daily.service
# systemctl restart apt-daily.timer && systemctl list-timers | grep -P 
"NEXT|apt"
NEXT                         LEFT     LAST                         PASSED      
UNIT                         ACTIVATES
Fri 2017-04-21 03:48:18 CDT  16h left Thu 2017-04-20 11:42:55 CDT  4min 4s ago 
apt-daily.timer              apt-daily.service


** Bug watch added: github.com/systemd/systemd/issues #3233
   https://github.com/systemd/systemd/issues/3233

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https://bugs.launchpad.net/bugs/1615482

Title:
  apt-daily timer runs at random hours of the day

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