I know what genetic bottlenecks are. I know what conditions bring them about. All I am saying is that you are making two assumptions that keeps you from understanding how it could have been a non issue in the past. #1. You assume that evolution has always occurred by the mechanisms observed in laboratories today. #2. You assume that lack of allelic diversity has always been detrimental.
You can reach today's levels of allelic diversity in 200,000 years. Show me where I am wrong. It doesn't take a genome that is ten times larger than today to generate the vast diversity of species we see from a few common ancestors. My evidence? That would be impossible to gather. My reasoning? You can generate a vast amount of diversity simply by turning genes on and off at different times in the womb and in development. It would not have to take generating new alleles to do this. The different alleles would come about later on after thousand of species had already speciated from their common ancestors.