Nether. It's about 10% of the ship cap versus 10% of he ship cap. Sen with that it takes about 45 minutes to run, there's no way we could do full ship caps. That undervalues swarm units, but we factor that as we're hand tweaking after.
Yea, I can think of four cases where the 10% ship caps vs 10% ship cap would not be equivalent to full ship cap vs. full ship cap.
1. When a ship has a ship cap <10, as such they could not have true 10% of their cap, have 1 ship (which is more than 10% for ship caps <10), and thus over-perform a bit in the simulation
2. Multi-shot and AOE type damage
3. Effects aside from damage that stack (like armor rotting, paralysis, etc)
4. The balance between high ROF with low base damage and low ROF with high base damage is not the same (lower numbers makes higher base damage more valuable, higher numbers makes higher ROF more valuable)
But as you said, you are already try to consider these things when balancing.