I think you are on the right track, and the BB is kicking in. Even though that article is rather old, I personally cannot find much research that correlates ammonia concentration to pH, while the relationship of ammonia's toxicity @ a given pH is well understood.
We are also in agreement that with the 'silent' cycle the plants should go hog-wild on ammonia. That's the same idea as using, say, urea, to cycle the tank. My concern for you, and before that, for myself was the amount of ammonia present: at 4 it's more likely to kill the plants and BB before it gets consumed. Therefore, my 90% WC, even though my tank was wall-to-wall with fast-growing plants.
Having a male dog has it's benefits: not many terrestrial plants survive his 'attention'.
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