Yes, editing ~/.config/swi-prolog/xpce/Defaults font.scale did the trick (almost). I had to remove the leading ! (having forgotten the conventions for X11 config files).
I’ll have to do some more fiddling to get the debugger help displaying at a size I like.
@jan - if the debugger help is available in the SWI-Prolog online documentation, I couldn’t find it and “grep” only found me xpce/prolog/lib/trace/pltracer.hlp.