I believe pH drop from c02 can harm fish/plants, it just depends on where you start at, how much c02 used, and how low it drops over the day.
Some fish species appreciate acidity to an extent, some don't, and plants ability to access nutrients can also be negatively affected.
I'm not sure which rocks are best for pH buffering. But remember the c02 creates acidity only while it's running and goes back to normal (I believe) when it's turned off over night.
Adding alkaline decor may create an alkaline environment so you may want to experiment slowly, depending on what fish you keep.
River water in nature have pH around 5.5, not to mention black water river.
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All rivers are 5.5? There's huge variation. In that variation comes waterbodies with fish and plants, some without, and everything in between. Nature is varied, just like what is feasible in an unadulterated aquarium.
Many plants won't live in a natural black water lake/river due to lack of light penetration.