Mounted on high tech ships though, as the first thing to hit, its most likely hitting pristine shield at range 900. If I were designing a slow armor eating weapon, and I wanted it to get a head start, instead of longer range, I'd give it the Ion Beam and Tachyon Lance treatment. Perhaps if the target's hard flux is over 50%, give it some chance for a portion of the scripted armor damage to leak through the shield like an ion arc. So by the time shields do go down, some armor has already been stripped.
That's an interesting idea! Though that also gets into "there's not actually any real counter-play" issues, possibly. Hmm.
I'm not positive its good, but it'd be the first approach I'd test. If we scale back to a range of 600 or so, then counter play is probably range.
As long as the bleed through is only scripted armor damage, and no hull damage, the counter-play is also just keeping your shields up. The enemy shooting you has sacrificed an actual shield damaging weapon slot with a slow acting armor eater. Most ships would probably be better off swapping out for more shield damage, and slap on a few high explosive missiles, like Reapers, Hammers, and Harpoons. That means you should be winning the flux war, unless you were already in a losing position to begin with. You can also mitigate it somewhat if the disintegrator "arcs" are similarly random like the ion arcs. At which point you're doing a little bit of armor only damage to the entire ship instead of in one area. So maybe a bit like Hydras in that respect.
I guess my counter question is, what do you see as the counterplay to an Ion Beam or Tachyon Lance? Here, the Disintegrator is doing far less shield DPS (62.5) than most medium slot weapons, and at a terrible damage to flux ratio, so it is not that different to hitting with just soft flux weapons.
In any case, if the shields never go down, then it doesn't matter if there is no armor underneath.
Or take that line of thought further, what is the counter play to a Cryoblaster (1400 Hull DPS) or Volatile Particle Driver (capable of 3000 burst shield DPS and 900 sustained)? In the case of the Cryoblaster, it is having shields and armor, and staying at range. In the case of the Volatile Particle Driver, it is having a lot of armor and hull. In the Disintegrator's case, it is having shields and hull, and if we leave the range lower, staying at range.
I feel like in the vanilla game, dealing with armor is a solved problem with common weapons, due to presence of missiles. Reapers, Hammers, Harpoons, and even Breaches will burst down or eat away at armor extremely quickly, and without needing to wait. And they can also serve to force and overload once shields are high. I think the thing to ask is, is eating some armor through high flux shields slowly at short range going to be better than firing a Typhoon Reaper (1 of 6, or maybe 1 of 12) at that same high flux ship? That it is what an anti-armor medium slot needs to compete against.