I played i bit with TC and really enjoyed this one, but its sad that you can't play with these others, including Vayra that brings good features.
Yeah that is the downside of the combat changes being so universal it is really hard to make Vanilla-modified mods work well. It would require an entire rework of almost all the ship files to make it possible, and then balancing for actual fun would be some serious math.
Stuff like: (hullsize weapon count) * (Avg dps of large weapons across vanilla and mods / number of average additional Archean Order large weapons(by hullsize))
So each Archean Order weapon would have to correlate to a certain fraction of vanilla damage (since there are more of them per ship) and then the number of weapon slots and fighter bays per hull (by hullsize) would have to be standardized against vanilla (and alongside other Archean Order ships).
Archean Order was not designed under these strict parameters. It was quite honestly designed for "fun" in the sense of cinematic battles that look similar to Star Wars battles. The weapons and ship mounts were mostly designed around aesthetics and then balanced afterward. I would not recommend this approach for normal game design, but for a mod its a design choice that I can make confidently and fine tuning over many years paid off in the long run.
For instance, the Megalith went through ~40 different looks before the mod was released the first time. I watched every video I could find of a Lucrehulk battleship firing a spread of lasers and wanted the top-down forward firing of the Megalith to look very similar. The weapon placement is key to make that happen and so the Megalith (as one of the most powerful ships in the mod) was the cornerstone that most of the other ships were balanced around rather than that being the consideration while designing weapon placements.
Archean Order weapons were then designed partly around the Megalith's weapon slots. That is why they are the longest ranged weapons- the Megalith has forward-facing weapon slots practically at the back of the ship lol but that's required to get the firing look it needs. Most weapons also have a very slight firing delay that differs from weapon to weapon. Again this is purely aesthetic because it creates the staggered fire iconic to Star Wars instead of salvo-based volleys that are more in line with WWII naval combat.
That should give some insight into the combat changes and why they are difficult to revert back to Vanilla standards.
I'm not done adding ships and weapons to the mod though, so if there are any ships and weapons from other mods you would like to see in Archean Order let me know (Permission from the mod author will be strictly required of course) and I can rebalance them.