HIG conforming application must use 12 pixel spacing and ignore screen dimensions. It sounds broken by design.
On PDA devices, screen size is one of most limited resources. GNOME HIG proposes constant spacing  , which keeps empty 20% or more of available PDA screen area in an average window. The cost: unneeded scroll bars, less items displayed or even unreachable rightmost items.
As an example of the result, please look at GTK file selector on 240x320 screen.  Even if it is not designed for small screens, it could look much better if it would not follow current HIG rules.
Very similar problems can be reached on high DPI devices, where 12 pixels means too narrow spacing.
HIG small device specs:
- Prohibit pixel based dimensions in ["HIG"] and similar standards.
- Predefine several spacing variables for these purposes and propose its use everywhere it is appropriate. These dimensions should be changeable by a standard gtkrc way.
- Modify GTK+ and GNOME to use these variables instead of constants 6,12,...
- If window size is not sufficient, propose using of scroll bars. Recommend space saving layout if the standard one would need scroll bars (e. g. use more tabs, constant number of checkboxes for line).  
- For small screen devices prefer larger windows without scroll bars over smaller (e. g. statically sized) windows with scroll bars.
There is much more things which can be proposed for comfortable use of GTK+/GNOME on PDA devices with small screen, no/limited keyboard, stylus instead of mouse and so on, but upper mentioned changes could be a good starting point. Maybe even gtkrc configuration option (something like "pda_mode" or so) for selected widgets would be useful for GPE and similar toolkits.