Two things occur to me from what you've said.
You mentioned API tests. Some people never see the yellow of zero with the ammonia tester, even with tanks which have been running successfully for years. The only explanation anyone can come up with is different people's eyes don't work exactly the same. There's also the room light. Daylight is fine, as are incandescent light bulbs. I think halogen and LED bulbs are okay as well. But fluorescent lighting - strips or compact fluorescent bulbs - make the liquid in the tube look greener than it really is.
Then there's the pH. As you've noticed, there is very little of that 0.25 reading which is free ammonia - 0.0004 ppm. The overwhelming majority is ammonium. With that pH, an ammonia tester reading of 0.25 is harmless to fish.
You mentioned API tests. Some people never see the yellow of zero with the ammonia tester, even with tanks which have been running successfully for years. The only explanation anyone can come up with is different people's eyes don't work exactly the same. There's also the room light. Daylight is fine, as are incandescent light bulbs. I think halogen and LED bulbs are okay as well. But fluorescent lighting - strips or compact fluorescent bulbs - make the liquid in the tube look greener than it really is.
Then there's the pH. As you've noticed, there is very little of that 0.25 reading which is free ammonia - 0.0004 ppm. The overwhelming majority is ammonium. With that pH, an ammonia tester reading of 0.25 is harmless to fish.