Believe me, I understand the math on this extremely well, as you should know since you've basically proved my math correct. You said only 4 waves could be present at a time and that is incorrect. Using an assumption that "well, one wave isn't going to be in range anyway" to explain that away isn't the way to go about a discussion. Someone reading your post might have reasoned out that same assumption themselves, but since you didn't say anything they would then be reducing the wave size from 4 to 3 and suddenly they think the DPS is 25% lower. I presented best case numbers in a variety of situations so each reader can make such assumptions without tripping over my own.
When talking about units in general, it isn't useful to fully spell out and explain every corner case. That's why I don't include damage multipliers - it makes comparisons too complicated. Yes, technically, you could compute the damage times multiplier times the likelihood of encountering that hull type. But that's a theoretical number that will never actually match the in-game reality. So it shouldn't be used.
As for the armor piercing DPS, it works like this: You increase DPS to account for the optimal situation where no AP is wasted. That is the maximum DPS before armor reduction that attack can deal against an optimally armored target. When you compare two attacks, you can look at the AP DPS to see how they compare against armored targets. When considering DPS against a specific target, you calculate the -DPS for the armor value against each attacker. This gives you four very clean DPS values to compare. You can optionally split the +DPS from AP into a separate number and reduce the -DPS from armor depending on what angle you are analyzing the date from.
If armor were a universal, with only the relevant value changing, I think this might be a more useful approach. But since somewhere between 1/3 and 1/2 of all units have zero armor, I don't think this is a concept useful for general case discussions.
The big problem is by attempting what you are here is that you are giving numbers that overestimate the usefulness. I very much prefer to use the general case, assuming the target has no armor, rather than cobble together a range of values that would still require the reader
Regarding the test, did you seriously expect two lone starships to stop a wave? I don't believe I said they could. I'm pretty sure I mentioned using 48 Spider Turrets as well.
In your own defense sample, did you compare the results of the same attack with and without Enclaves? That's what I did, and I showed that it was the turrets, not the Enclaves, that did the majority of the damage.
You described clearing a Mk II planet on 10/10 with 120 ships plus Guardposts plus Guardians using just a pair of Enclaves. Why would I not expect those same enclaves to be able to kill a mere 75 or so fleetships?
What the Enclaves have done is open up your early game to give you more options to carry on with later. Enclaves will not win the game for you.
I think overall, this is what Cinth and I are saying. Enclaves are useful. They are not OP units that produce an instant win, or reduce the game to trivial difficulty. The AI has direct counters for them (OMD, Arachnid GP, Disassembler, Eyes) that are not minor.
I've got a game going on right now with this: A Neinzul unit and the MSDs. Far more powerful, and more numerous, than mere Enclaves.
Really, if we're talking OP units, the SSBs, Blade Spawners, Protector Starships, TDLs, LTFs, Corvettes, Fireflies, Sentinel Frigates, Shield Bearers, and Spire Starships are all much more overpowered. Just off the top of my head.