It is kind of a no-brainer that from a naturalist or purist point of view, the best biological substrate for a reef tank would be the actual rock found on a coral reef. It contains many strains of healthy bacteria that have been proven to be absolutely beneficial to the biological stability of a delicate marine system. Not having these bacteria will increase the chance of nuisance algae and pests from taking hold, especially in the chaotic and unbalanced nature of a new tank. The reality of reefing today means experimenting and trying different substrates since live rock is almost impossible to find, and also quite damaging from an environmental perspective. (This is a whole different topic) After-all, the rock itself, whether live or dead really is inert so as long as the material is not toxic or causing other detrimental issues, we are really limiting our conversation to the effects of biological seeding via live rock vs biological seeding vs alternative methods.
When all the pros and cons are weighed I think there is a growing argument to choose a live rock alternative such as Marco Rocks. Closer attention will have to be paid to the biological balance of the system and it has always been Marco Rocks stance to go slow, seed with bottled bacteria or with bacteria inoculation from an older, established system, etc. I personally think people start up a tank and lack the patience that it needs to slowly mature. With my own tanks, I use dry Marco rock and leave the lights off for the first month or two. I run all filtration but do not add fish. I feed the tank sparingly and seed it with a few pieces of rock from an older tank. Snails or urchins can be used to keep the minimal algae growth in check. They also kick the detritus up and into the water column where it can travel to the filtration. Not keeping fish in the tank allows the copepod and micro-fauna to absolutely explode. After one month it will look like a copepod tank. They will become the apex animal in the tank! Utilize extra strong flow during this stage and just let the tank become stable. Up the feedings as the algae becomes more and more encrusting and calcified in nature. (Harder to remove from the glass is a great test)
The rock will become coated with a biological film that will inhibit the growth of unwanted algae/dino. Should you see a dino outbreak, UV sterilization has been seen to be quite effective. (For many common strains).
At the end of the day it is a personal choice of what substrate to use but if done right, many of the problems mentioned above can be avoided in part or entirely while also feeling great about not having wild rock ripped from the ocean to start your tank."