So i've achieved a base-level method to sync >1 wiki's settings, thought i'd reply to my own post in case this helps someone:
The fundamental thing about TiddlyWiki Tones assumed I completely understood above was that dragging a link to a tiddler from one TiddlyWiki into another (such that you get the import bar popup at the top of the screen), causes the contents of the linked tiddler to be imported (after a confirmation dialog). It doesn't matter whether the linked tiddler is text/images/settings/code/plugins. This is a fundamental and astonishing magic of TiddlyWiki, and though an inexperienced user might use and see this in action from instructions etc, it can be difficult to appreciate just how all-ecompassing this ability is.
So what's a 'link' to a tiddler? Well it can just be as simple as the name of the tiddler from your 'open' or 'recent' sidebar tabs, just drag any link from there from one TiddlyWiki into another (this works regardless of whether one of these TiddlyWikis is on the internet and the other is on your filesystem, or if both TiddlyWikis are using TiddlyDesktop, and so on...). But Tones was specifically talking about, for ease of collecting settings together, making a link to a tiddler IN ANOTHER TIDDLER: by either just stating the name of a system tiddler like $:/themes/TiddlyWiki/vanilla/metrics/storyright or linking to another tiddler name using the [[double square brackets]] notation.
Another thing I guess Tones assumed I knew there was that every setting as you see them in a TiddlyWiki's control panel is stored each in an individual tiddler whose name is availble by just clicking on the setting name - this is an axiom of TiddlyWiki: we atomise individual things to individual tiddlers; so where I was worrying that i'd have to mass-copy all the setting in a TiddlyWiki's control panel (and that would include things like the wiki title which I don't of course want to copy), instead we come from the opposite trajectory: we look at the individual things that have changed from the standard settings and just drag the link to those (for instance the example I just gave: $:/themes/TiddlyWiki/vanilla/metrics/storyright - I changed the setting for 'how far the left margin of the sidebar is from the left of the page' from an absolute value to a percentage). So its easy, once you know what you changed, to make a list of links.
Once I grokked those things, the first option Tones gave me above makes sense: 'make a tiddler with just links to other tiddlers and drag the links' - well really the level of automation i've got so far is pretty much that, though its a bit flowery as I've made a kind of diary of what settings I found I needed for what I consider my 'standard' style (and where I got the ideas from etc), and in each section, when I worked out for each setting what tiddler it relates to, I've put a link to the setting tiddler(s).
So i've ended up with something a bit like the 'master-slave' relationship Tones was envisaging there, since I have a tiddler in a wiki that lists my 'master' settings, and i'm using that tiddler for each new wiki I make. Since i'm not intending to create the industrial number of wikis he has, I'm happy with just that really: although I'd point out my 'diary' tiddler of settings is also a symptom of me not really finding a good answer to my other original question of how I can diff changes already made to >1 wiki: I couldn't do this programatically and just had to start again with a standard TiddlyWiki and customise it whilst documenting settings I changed - time consuming, but worth doing if only to realise that I hadn't actually changed that much
In terms of plugins, I didn't really list standard TiddlyWiki plugins in my 'diary' tiddler, because they're just listed so very nicely in TiddlyWiki's plugins section already - so I found as long as I considered these things, I can just look at any of my existing TiddlyWiki's plugins pages and just copy it:
* I had overwritten some 'shadow' tiddlers for a plugin or two, but I decided to just try to live without those customisations for ease of replicating plugins (its easier to know i'm using the stock plugin than potentially using something that includes prior customisations i've long-since forgotten I made)
* there were some plugins I just decided I didn't need, just keep the list of installed plugins small
* with codemirror, I just installed everything since I use a lot of things and installing everything is easier to remember than excluding the few things I don't need
As you can see this is all a very basic solution that reflects where i'm at with TiddlyWiki, in particular if my plugin needs were more complex it would be time to continue exploring Tones' options for automating synchonisation using bundlers/packages and so on, but I thought it worth documenting the basics. Tones' other options are all further enhancements of the 'list of links' functionality, but that functionality in itself is very powerful to begin with, and may be enough for you if you don't have 100 wikis