I guess I'd point you to the Wiki for Gizmos, then. See
http://hlkitwiki.wolflair.com/index....ies_and_Gizmos for the base definition and it's covered a bit in Bootstrapping at
http://hlkitwiki.wolflair.com/index....tle=Bootstraps.
For the real use-case I found it under Vehicles where trying to bootstrap things like weapons and such wouldn't work, you have to put them in as a Gizmo. So this is where I found the most useable example of that:
http://hlkitwiki.wolflair.com/index....hicles_(Savage)
To be honest I've always had more of a tendency to want to just get the coding part over with so I've always been a bit less concerned about the reasons why something is done some way (or even, at times, what it means) and more about just that it works. So you might need someone like CC or Mathias to get into the nitty-gritty of that side of it.
As for Sci-Fi, it adds quite a bit of stuff, including tabs for power armor, cyberware, robots, lots of extra bits.
Finally, on magic items while I've certainly done some, probably there are a few in the Deadlands Noir setting for example, for the most part I don't think I ever really did anything more than use them like they were Edges. So any bonuses would just be coded on a piece of equipment the same way I would do it for an Edge and I didn't use any Gizmos with them. (As a side note I'd probably say DLNoir is probably the most complete of all the data files I've made and can be useful for examples. The other one that's my go-to especially for vehicles, which use Gizmos and such, is Weird War II. I would probably also recommend the High Space files, as well, just because jbear did some really cool finagling of things to make a data file that changes things up to be able to make ships as the character in his ship building data file, which I thought was pretty cool.)
That's probably especially true when making a settings file for general use because you can't really assume that someone has the Companion add-ons so working within the basic framework is usually best to make it accessible to the most people. Not all modules are like that, I think High Space requires the Sci-Fi Companion, for example, and I know Necessary Evil requires the Super Powers Companion. I think Interface Zero will also be one that requires SFC while I think Rifts will need SPC. But where possible I, personally, try to make settings without assuming the need for a Companion.