The problem is two-fold:

1.
The clock-applet will try to force the system timezone to the timezone of the 
location you are trying to set as home.
(This is really awkward for international minded people who have long since 
abandoned local time in favor of world time)

2.
the clock-applet does not accept direct timezones settings in tzdata (the Etc/ 
range)

No. 2  foils a possible workaround: 
I tried to edit my home locations timezone to 'Etc/UTC' so that it matches my 
system timezone and will thus resume displaying my local weather in the 
taskbar. Unfortunately the clock applet seems to be ignorant of the presence of 
direct (non-geographical) timezone input and will not set the locations 
timezone to 'Etc/UTC'

@Sebastien: Yes, I think the clock applet should be able to function
fully without it trying to force a change in my system time. An elegant
solution would if every defined location's weather could be optionally
set to be displayed in the taskbar. This way the inability of the clock
to acknowledge the 'Etc' set of tzdata would not inhibit users from
seeing their local weather :D

-- 
weather not shown in world-clock-applet when computer timezone differs from 
home location timezone
https://bugs.launchpad.net/bugs/232375
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