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there are several ways to do it.
it much depends on the final user interface.

right now what i've got working is the standard server script
with the "-c" service option providing it is the *first* option
in the opt list. the configure options ("-p","-n") aren't
working at all so you have to modify the "address = ('',8888)"
line in roundup_server.py and the TRACKER_WEB dict in the
same file to meet custom needs. options -d -l must be
provided just to conform to validation piece of code and
to distinguish from background/foreground startup.
the limitations i mentioned are due to the *minimal* changes
i made (less than 10 lines) but resulting in a server able
to be installed, removed, started and stopped either by
command line or thru windows' control panel.
basically, what i did was to separate the "-c" optargs
from the rest and send them to an appropiate call of
win32serviceutil.HandleCommandLine()
i'm attaching here my version of roundup_server.py for your
best convinience.

some alternatives for server customization that i can
imagine now are:
a. use the same command line options. say:
   C:>roundup-server.bat "-c install" -n SERVER -p 8765 ..etc..
   
b. use an external custom parameter file, something along the
   lines you did in trackers/config.py. say:
   C:>roundup-server.bat "-c install" -f 
c:/roundup/websrvcfg.py
   
c. use module variables in roundup_server.py.
d. do nothing :-)

for alternative a, we have to rearrange the code because
RoundupService class will have to parse the options at
*execution time*

fyi, whatever we do the server needs to modify and read
the registry. not a problem because those custom keys will be 
under
the Roundup Service registry subtree.