We are also looking at the number of cell types in an organism
Well, no, we're not. The function of proteins like cytochrome c or ribosomal subunit 16S aren't related to cell type, because the function is so basic every kind of cell in every kind of organism needs to perform it. All of your cells, regardless of type, are engaging in protein synthesis and electron transport activity, or else they're dead.
Cell type and cell diversity is going to have no effect whatsoever on these highly conserved proteins, and that's how we know that accumulated differences between homologous genes in different organisms really do reflect evolutionary time. For other proteins, that's not going to be the case, but those aren't the proteins being used to construct phylogenies.
If genetic equidistance is the result of the epigenetic complexity of organisms
Well, but it's not. We know it's not because, again, genetic distance is being measured only on genes that have nothing to do with cell type, cell diversity, or epigenetic complexity. Genetic distance is measured on the genes for cytochrome c and ribosomal subunit 16S (among others) and the function of those proteins is identical in all species and all cell types, regardless of the complexity of the cell or of the organism.
That's why they're such a useful basis for constructing phylogenies; selection for different function in different species is utterly taken out of the equation. Thus we can conclude with certainty that the genetic distance observed between these homologous genes is not related to the complexity of the organism. Regardless of how complex an organism you are, your mitochondria engage in electron transport and your cells express proteins.
Yes it is, because how are we supposed to tell if the genetic equidistance phenomenon is the result of the time lapsed since divergence or if it is the result of the epigenetic complexity of organisms?
By only measuring the genetic distance on proteins that have identical function between the compared species regardless of complexity, like cytochrome c and ribosomal subunit 16S.
With respect, you have not specified any method of how we are supposed to do that.
Yes, I have.
However, in this particular case, I think I do mean "equidistance."
In many cases you do mean "equidistance." But in most cases what I think you actually mean is "distance", as in the genetic distance between two species. Equidistance is an observation about the genetic distance between each of two different species to a third outgroup, and the fact that this pattern is observed in highly conserved genes supports the concept of molecular clocks and, by extension, evolution.