The Chinook is a combat tanker it can fight back compared to a Phateon It have better combats stats (Hull, armor, speed, Flux and Vent), Its gun arc and system allow to support the front line and fight other small ships, It is closer to a cheapper Mule, 6 OP instead of 7 but made for Fuel. For me the ship is okay but suffer of a smaller OP pool than most 6OP destroyer, a Buffalo mk2 has 70 and cost 4 OP. 40 OP is a bit too shoprt for a semi fighting ship...( lets say we put 2 LAC and one LAG one vulcan in the back , that already 17OP half of the ship OP pool, you will have a hard time maxing its vent/capcitors or put any hullmod on it!
The Mule is genuinely strong ship. It has 650 armor, 5500 hull, 1.0 shield and 3000 flux capacity, 60 speed and Maneuvering Jets, and a medium composite turret on top of the small ballistics and missiles. It is leagues above the Chinook, which in-combat is basically a slightly more durable Phaeton. 400 armor, 3000 hull, a 1.1 shield with 2750 flux capacity, 50 speed with no mobility system, and worse armament than a frigate does not a combat ship make. It is genuinely an awful idea to deploy the Chinook as a support ship just because it has Active Flares.
Once again if we compare it to the Mule its smaller and cost less OP 5 against 7. Its size+system+gun placement mean it can hold the line with the boys while spamming flares. Once again for me its problem is OP pool for a combat freighter. 40 is very small for a ship that will need guns and capacitor and vents... with so little except if you build in mods it won't survive above the early game...on the other side very few cargo ship come without the civilian hullmod and not at this price range.
The Stratus's stats are even worse than the Chinook's. Less armor, less flux, fewer slots, slightly higher hull and speed. It's just not a combat ship. I don't know why you think it is. It can't stand up to any combat frigate that isn't d-modded pirate trash.
For the Cyrus its problem is it ridiculously small OP pool the rest of the ship seing its size, shield and gun placement that is easier to exploit than the Valkirie(almost fully pointed forward on a very long ship), but I understand why its this way , Its a Condor and Valkirie in one ship for 6 OP hard to get this kind of stuff any cheaper. its very cheap battle carrier for ground support and raids. Hard to find reason to ever make it better if its DP price doestn go up to 10 Supply or more.
Conclusion, I would not change the Cyrus or he would make stuff like Condor pointless. As I said it is a ship that fill multiple role in the fleet, if he was anyn stonger it would invalidate both the Valkirie and the Condor, no possible change here except if the ship get costlier to use...
The Cirrus can point a whole two small hybrid slots forward. It does only have 3 small weapon slots, so I suppose saying that it can almost fully point its whole armament forward is technically correct, but I think that's a bit misleading. The Condor is the most efficient fighter bay per DP carrier in the vanilla game, at 1 bay per 5 OP, and brings a medium missile with fast missile racks on top of that. The Cirrus has 1 fighter bay for 6 DP, efficient but not amazing considering the ship system is Active Flares, has a forward armament of 2 small hybrid slots, and is generally not good.
But the Stratus and Chinook a pure shooty boat, personally 50-55 OP would be a bit better of a deal. They have good stats , form and gun arcs but they cant exploit them because they are so OP starved, but they should not end up superior to a Mule or Mule (P) that are costlier to use.
As you have said, the Stratus and Chinook are OP starved. They're also undergunned, underarmored, underfluxed, and not good combat ships. The Mule is a solid combatant with heavy armor, high missile strike potential, and plenty of OP. It is in no danger of being worse than any of Diable's logistical ships.
As to the implied contradiction between these items, I honestly just don't buy it; imo you don't even have to try hard to have it all make sense in-fiction.)