Дебиан: Как изменить параметры запуска эмулятора терминала, не прорушив структуру меню и систему альтернатив ?

Смотреть на ресурсы. Например, у меня xterm запускается всегда как login shell:
~> grep -i xterm .Xresources 
! XTerm-color 
XTerm*LoginShell:       on

Если б я хотел reverse video, ...
       reverseVideo (class ReverseVideo)
               Specifies  whether  or  not  reverse video should be simulated.
               The default is ``false.''

то сделал бы XTerm.reverseVideo:       true

man внимательнее читать!

RESOURCES (available also as long-options)
       Note: "rxvt --help" gives a list of all resources (long  options)  com-
       piled  into your version.  If compiled with internal Xresources support
       (i.e. rxvt -h lists .Xdefaults) then rxvt accepts application  defaults
       set     in     XAPPLOADDIR/Rxvt    (compile-time    defined:    usually
       /usr/lib/X11/app-defaults/Rxvt) and resources set in  ~/.Xdefaults,  or
       ~/.Xresources if ~/.Xdefaults does not exist.  Note that when reading X
       resources, rxvt recognizes two class names: XTerm and Rxvt.  The  class
       name  XTerm allows resources common to both rxvt and xterm to be easily
       configured, while the class name Rxvt allows resources unique to  rxvt,
       notably  colours  and key-handling, to be shared between different rxvt
       configurations.  If no resources are specified, suitable defaults  will
       be  used.  Command-line arguments can be used to override resource set-
       tings.  The following resources are allowed:

...

Так и создать...

~> tail .Xresources 

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! Xpdf
!
*Xpdf*fontList:  -monotype-arial-medium-r-normal--12-*-*-*-*-*-koi8-r

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! Display
!
Display.font:            -monotype-arial-medium-r-normal--12-*-*-*-*-*-koi8-r


Все, при следующем запуске Х он будет учтен. 
Для принудительного прочтения - 
~> xrdb -merge .Xresources