Well as my Mac OS 9 brain is struggeling every time I have to use Linux, I like to help in your opposite situation as far as possible.
Been using Linux as my main OS since 2001, never got warm with Windows besides where i had to, ie. gaming, and was too poor for a Mac back then. The G4 i now installed we got for free when my fiances former company threw it out, they had used it with BitFonter to create fonts for various mobile devices back then, some holy "Don't upgrade!" machine they kept for compliance until that was from the table. Then my fiance had it in storage until i stumbled upon it and did the only reasonable thing a fiancee can do, that thing is now mine.

My background, i got my first very own PC, a used 386 DX40, in 1992 when i was 8 and around 96/97 i was still using my trusty NovellDOS 7 and Geoworks Ensemble setup before i finally had to switch to Windows 9x.
Nowadays i have a bunch of retro machines running 98 or XP respectively but all my productive machines run some variant of Debian or Ubuntu, with my abused as a desktop Steamdeck running the later. Can't beat a modern system using just 15 watts max, especially with German energy prices. The whole setup with two screens and an amp uses ~35 watts on idle. ^^'
The only thing you are doing usually with "preferences" files is to backup them in few cases, or to delete them when a program, driver, etc. went crazy. Usually it gets written new at new bootup of the system, or a restart of the program in question.
Like @Mat pointed out, these files are not text files nor anything to be usually edited directly: it is the actual settings, as in, the settings values, of a given program, stored and used by the program in question. So for example "Keyboard Settings" are handled by the "Keyboard" Control Panel (a type of "app"), and if you want to change the settings, you do it through that.
Noted, so i can assume copying that directory is more than enough to back up all settings?
The solution is an self-extracting archive
Start witht this Stuffit in ".bin format". It is the DL number 4
https://macintoshgarden.org/apps/stuffit-expander-55
Yeah, already got that sorted out, Macintosh Garden might be a mess to comb trough if you don't know what you are looking for but it is a great archive.
I tried a timedemo of Quake 3 on the G4 to ballpark the performance and got a respectable 75 fps in 1024x768 32 Bit colors for a retro machine.
Actually, there's essentially nothing that needs to be opened through the Apple Menu, since it's just a collection of shortcuts. Also, I assume you mean the "Control Panels" menu item, rather than "Settings"? There's no "Settings" menu item. Keep in mind just about any software, in Apple Menu or not, is eligible to create a settings file and store it in the "Preferences" folder.
Oh, so like any modern OSes start menu? That raises a better question, how can one add a menu item to it?
StuffIt Expander is included in all of Ross' Mac mini G4 CDs, because it is included officially with Mac OS 9. Ross' CD is a CD to install Mac OS 9 with, and so includes helper apps to achieve that. The installation process is done through the restoration of a Mac OS 9.2.2 disc image, inside of which is StuffIt Expander and everything else. If you really want to use it without installing and rebooting into your newly-installed Mac OS 9 partition, then you can simply just mount the image that is used for restoration/installation, and find and use StuffIt Expander from there.
I couldn't find it and .sit files where not linked with any program.
In the end i found a version that was stored as a BinHex file, .hqx, and got it installed trough that.
Still find it funny that everyone had their own standard archive format, DOS/Windows people have mostly Zip, Amiga people have LHArc, Mac people have StuffIt, Linux people have tar.gz and so on.
Hope this helps, and let us know if you need further help.
There is one thing that would make me feel right at home in Mac OS 9, it would be nice to have an orthodox file manager, vernacularly called Norton Commander clone. Used these since my childhood and they are always a nice tool to have around for massive file operations.
What options does one have with that?