Pelo Manual , parece que a opção -clip
parece fazer o que você quer:
-clip WxH+X+Y
Only show the sub-region of the full display that corresponds to the rectangle
geometry with size WxH and offset +X+Y. The VNC display has size WxH (i.e. smaller
than the full display). This also works for -id/-sid mode where the offset is
relative to the upper left corner of the selected window. An example use of this
option would be to split a large (e.g. Xinerama) display into two parts to be
accessed via separate viewers by running a separate x11vnc on each part.
Use '-clip xinerama0' to clip to the first xinerama sub-screen (if xinerama is
active). xinerama1 for the 2nd sub-screen, etc. This way you don't need to figure
out the WxH+X+Y of the desired xinerama sub-screen. screens are sorted in increasing
distance from the (0,0) origin (I.e. not the Xserver's order).