Hey lochar I can understand why this is all a bit confusing and unnerving.

Good points you raise, I didnt follow too much what's wrong with armor upgrades and my manual is sitting unopened in another country (had to move for my job). But I typically think that's something that's been fiddled with a lot for game balance, and that is now working to the developer's satisfaction, but not quite as envisioned during game design.

Anciliaries and swapping I think are working as intended in game design, they just either thought this was too insignificant a feature to make it to the manual (the infamous clause 6 in my above post), or they wanted us to figure it out for ourselves. It is after all a function that only the most hardcore micromanagers will regularly use.

The spy and assassin thingy is a combination of all. Looks like the feature (assassin hindered/helped by spies) is working in a fairly logical way, but was left out of the manual for various reasons (insignificant or tweaked after the original game design). What got broken in the process however is the success rate display I think.