Ah, ok, thank you for clarifying! The AI is the same across all ships, so that wouldn't actually be a confirmation one way or another; e.g. it's entirely possible for a mod to mess with ship AI across the board, affecting the behavior of vanilla ships, ships from other mods, etc.
I'm going to move this to the modded section. It'd be helpful to see the list of mods you're running with!
Honestly, this entire list runs excellently well, besides tweaking some outdated mod version files so they can run on .96a RC10 that is. It is ordered based on appearance in my currently used mods folder the game is running on so not necessarily perfectly alphabetical order.
Diktat Enhancement
Ko Combine
A New Level of Confidence (40 fast variant)
Amazingh's Ship Foundry
Adjustable Skill Thresholds
Advanced Gunnery Control
Adversary
Angry Periphery
Apex Design Collective
Apocrita Association
Aptly simple Hullmods
Bird's Collection
Bigbean's Ship Compilation
Bultach Coalition
Carter's Freetraders
Caymon's Ship Pack
Combat Chatter
Combat Activators
Commissioned Crew
Customizable Star Systems
Coherent Watermelon's Ship Pack
Detailed Combat Results
Diable Avionics
Domain Explorarium Expansion
ED shipyards
Emergent Threats
Epta Consortium
Exalted
Experimental Hull Modifications
Machina Void Shipyards
Extra Systems Reloaded
Extratential Lanestate Union
Star Federation
Fluff's Ship Pack
Fuzzy Ship pack
Grand Colonies
Graphicslib
Grytpype and Moriarty's Defense Authority
Hazard Mining Incorporated
Brighton Federation
HMI Supervillains
High Tech Expansion
Industrial Evolution
Interstellar Imperium
Junk Yard Dogs
Kadur Remnant
No Such Organization
Keruvim Shipyards
Kyeltziv Technocracy
LazyLib
Leading Pip
Legacy of Arkgneisis
Low Maintenance
Low Tech Armada
Luddic Enhancement
Luddic Enhancement IED
Lunalib
Magiclib
Mayasuran Navy
Missile Ship Overhaul
More Hullmods
More Combat Terrain Effects
More Military Missions
Nes's Ships and Weapons Pack
Nexrelin
Oculian Armada
Ocutek Pirates
Osiris Alliance
Planetary Shield Access Control
Planet Search
P9 Colony Group
Progressive S-Mods
PRV Path
PRV Starworks
Random Assortment Of Things
Roider Union
ScalarTech Solutions
Scan Those Gates
Scrapyard Armories
Seafood Shipworks
Secrets Of The Frontier
Ship and weapon pack by DarkRevenant
SpaceTruckin
SpeedUp
Arma Armatura
Starship Legends
Stop Gap Measure
Super Cool Faction Flags
Support Ships Pack
Tahlan Shipworks
Terraforming and Station Construction
Thog's Domain
Thog's Remnants
Tri-Tac Special Circumstances
United Aurora Federation
Underworld
Unknown Skies
Unusually Gullible Hullmods
Xhan Empire
That is all of them. All are in their latest version I could find.