Looking at 3.1 here...
When the system-configuration is unavailable, the actual defaults are topaz 9 for System Default Font and Screen Font, and topaz 8 for icons. I thought I'd mention this because for example, if no Prefs for fonts are saved via Font Prefs (ie no envarc font.prefs file at boot), then when you actually load Font Prefs it makes out that topaz 8 is currently selected for all three fonts which is false.
Indeed, and I fixed this. However, note that all 3.1 preference editors "do not see" the old intuition preferences system, at all. Thus, if you have a specific setting in S:System-Configuration, and the system loads it (it does), and then open any new preferences editor, the (non-standard) settings are ignored at all. This goes for all preferences editors, since 2.0 up.
As we probably all know here, system-configuration (with editor!) allows you to setup your basic prefs, even when you select 'Boot with no Startup-Sequence' in the Bootmenu via the system-configuration file, it's odd how Commodore included the file, but no editor. Is the file still there for 3.1.4?
Yes, of course, and there is no editor for it either, and this will not change in 3.2. Note that there is sufficient old, ancient software that boots from floppy, and provides an S:System-Configuration. However, usage of this file is deprecated, and it should no longer be used, and there is no preferences editor for it, on purpose.