but evolutions are stupid, and there's little reason to suspect that any religion is truly optimal for propagation

I think that religious memes are probably more optimal than organisms because successful ones can spread much faster, rely less on pre-existing machinery, can change faster, and because so many of them have been tried.

However, its also possible that we've simply reached a local maxima, and that our current memes are too strong for most upstarts but many upstarts would, with further development, be much more effective.

Overall, I'm inclined to agree with you that rationalist memes would need to be designed.

Rationalist memes probably simply wouldn't be selected for and would have to be designed, because of the fact that you're specifically trying to get someone to weaken the biases that make it easier for religions to stay together.