I consider gravel and rock to be areas where detritus initially accumulates.
Detritus is fish mucous, feces, dead algae and bacteria, bacterial floc and dead plant matter that falls to the bottom of a pond. Until a substantial amount of detritus builds up, the bacterial population and diversity does not exist that can completely process the organic matter.
I consider what is there to be a "young" substrate, one that lacks the the diversity to completely process the organic material into nitrogen and CO2. Because it lacks the diversity, excess nitrates are released into the water column, contributing to excess algae growth.
I am assuming that you are speaking of a new pond.
First lets clarify what is being discussed. Apparently what is being discussed here is the formation and maturing of the Benthic layer. A sub-strate is a too general term that can be applied to many submerged surfaces.
Within a few hours, the initial Benthic bacterial biofilm has formed and algae has started to grow, both sessile and planktonic. A mature biofilm will have developed within a few days to several weeks depending where the body of water is classified in the Saprobian System. All water contains some level of Nitrate and Carbon, both organic and inorganic, so initial biofilm formation and colonization is not usually inhibited. A new body of water (pond) will also immediately begin accumulating organic matter...plant litter, insect and animal feces, etc. which ensures a steady stream of nutrients to the developing periphyton whose growth rate is in direct proportion to these available nutrients. This is assuming that other factors such as DO, temperature and available light are at levels conducive for growth. In ideal circumstances, the dynamics of the Benthic layer and accompanying Benthos are sufficient in converting the detritus before it has a chance to accumulate to any great extent, but, over time, as the body of water becomes more Eutrophic the bacteria cannot, because of the limited amount of SSA, keep up, so to speak, with the amount of detritus that is collecting. This is the beginnings of 'muck' accumulation.
Excess Nitrate is usually extant because of the lack of live plant material (Macrophytes) at a level proportionate to the organic matter being added to the body of water, the result....algae blooms.
The composition of the Benthic sub-strate does play a major role with silt being the least desirable and wood being the most. Interestingly, in lab experiments, plastic proved to be a good sub-strate. One of the main controlling factors in sub-strate suitability is the size of void space within the substrate. Silt and Clay, though high in nutrients, possess the least void space restricting the passage of DOM (Dissolved Organic Matter). Gravel, on the other hand, has a large amount of void space which allows for fairly unfettered flow of nutrients. Wood, because it is totally organic and porous, blends the best of both. No naturally occurring benthic sub-strate is ever exclusively comprised of only one material. It is usually a blend of sand, gravel, clay, and rock dust and, over time, silt. This is basically the benthic sub-strate in my pond and what I have used in several client ponds.