Good points and questions, the resources growing right at the planet is a bug, it should be when they get back to the base and it's added to the total.
The other issue however is with the self replication part. I don't think the new clones are starting from the base, I had it set where they should spawn at a new planet and then head back to base, I'll double check on that. But you're right that this still doesn't really feel like the right behavior for the probes and more over the base is counterproductive.
They should be continuing outwards to new planets and not always going back home each trip. It'll be a big change but definitely worth it. I'll work on this as the next update