First off, I notice that I have 2 typoes in the modding tutorial.
"Our Ship in Sector" and "Our Ship in System" have this in their descriptions:
"This value supercedes the Enemy Ship in System value."
and they should not have that. I will fix it later when I get back home (in a few days
).
Now to your question:
My guess would be that se4 does not take the max change per turn values in absolute when dealing with such large numbers for anger modifiers (such as -3000, or 100 for each troop). If you can, run this same test on an older Version of SE4, to see if it was always like this, or if this is a recent change in the latest patch (could be a new bug or something).