The reason why the player can’t go extinct unless you die while playing yourself is actually a feature to stop people complaining. We already get quite many complaints from people saying they don’t understand why auto-evo wants their species dead. So as a special consideration the player can’t go extinct from auto-evo, just your population gets stuck at 50.
The player is not playing with all of the trillions of members of their species that live over the span of a 100 million years, so it makes a lot of thematic sense that auto-evo affects the player species. After all the player’s personal performance would be basically a rounding error (but as we are making a game the player’s performance is actually a pretty big part of the player’s total population).
With that ramble out of the way, I agree that auto-evo probably needs some extra attention to make sessile species possible. Which is again one of the reasons why day/night cycle is not enabled by default. That is tracked by this issue: