The mod didn't affect AI behavior all that much, except in a few specific regards. The acceleration of the victor is probably due to it detecting a hostile or unknown platform (or a platform on the same side making such detection) and a stock doctrine being run. The changes of the mod to sonar capabilities could cause this effect to show on the mod but not on stock, but it is stock behavior.
As for diving, I think the AI is programmed to change depth, sometimes to check the link and such. You might be able to fight this using scripts that force the sub to a certain depth for a certain amount of time, although a new doctrine that starts will probably override this.
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