Actually, what You need is fine sand at the bottom. In small aquaria, where the chemistry is unstable each decaying particulate create greater strain on the filtration. If the substrate consists of bigger stones, than each particle finds its way beneath the gravel and decomposes there. You don’t want that. This creates small timebombs of amonia. With fine sand there is no place for filth “to hide”, and so it decomposes in a more controlled way.
Even in the low pH there are some bacteria alive. In the sulfur stream in Spain, where the pH was below 2 (!) scientists found colonies of algae and bacteria. So don’t sweat it. There is some filtration.