I don’t know that I’d call literally everything we can eat ‘a few select species’. It’s not like humanity is native to New Eden. After all, the Amarr have records going back to pre-Dark Ages dating and the closure of the EVE Gate.
So, no, I don’t think it’s particularly odd that we don’t share a common ancestor with the microbial mats we find on thousands of different planets across the culture. If anything, I’d say the stranger scenario is having humanity on so many worlds before the (re-)development of space flight.