It doesn't matter too much if your eyes glaze over at the sight of those diagrams - they're all out of date by now anyway (although they're relationship diagrams, not data flow
)
Looking back at what I said, the basic weaponry option (for when people want to do it in a simple way) might be more workable already than I thought. If you use a ratio limit of "between 0 and 100% of troopers may take this weapon" then by rounding the numbers you can already handle the simple mixed equipment situation. The only thing it wouldn't cope with is more complex mixed equipment as "mutual exclusion group" (e.g. limiting a troop type to take X or replace it with Y or Z), which is what some units like Nobz would probably encounter.
I think I'm inclined towards the "contained units" as the normal way of doing it. There are three reasons for it:
1) Flexibility - you don't need any work-arounds for mut-ex groups on weapons
2) Power - you can handle things beyond Nobz Mobs and Nid Warriors. It would also be useful for Space Marine Command Squads where you get a command squad with any of Apothecary, Company Champion, Company Standard Bearer.
3) Story telling - if you've got something like a Nobz Mob and you've got each Nob as their own unit then you can name them and have them as their own character. A lot of gaming is about the story (for some gamers at least) so having them separated out would be very useful
As for it being how Army Builder does it, I wouldn't know as I've never really used it. Ideally I'd like to be able to have a plugin that can load Army Builder files in the same way as we can load Rollcall files, but I can see it needing quite a bit of work.
[edit] Topic split to make the discussion easier to find.