Hi Kai,
As I mentioned the problems I had were with a freshwater system years ago (however my reef systems with a deep sand bed and plenum) have had no problems and only require modest amount of upkeep to keep the system happy (ammonia =0 ppm, NO2=0 ppm, NO3<5ppm). (Good to hear that your studying this process, if I have questions I can refer them to you).
With beginners the issue may be better resolved if you could list particle size by designated trade name (ex. play sand vs construction vs pea gravel ect.) as an appropriate substrate.
The time I used sand and ran into difficulties, I wsa using play sand and that may have been too fine and compacted allowing anaerobic processes to set up. (after the fish kill, I stripped the tank down and upon stirring the sand bed was able to easily smell hydrogen sulfide).
Perhaps some of my point of understanding comes from the reef aquaria side where some of the information has been made less technical for the average aquarist hence my understanding of the reverse ammonification process (although in many of these cases the particle size used was too small and the lower depths of the beds went anaerobic/with a high organic load so you are correct that human error seems to be a big part of this ).
Thanks Kai,
Ed