this will not conflict with the storyline. He suggest an autocolonize algorithm where your ships would colonize planets you know of, not planets that are hidden from view (besides, steller cartography is THE cheapest tech in the game and is always researched early on, or traded for).
Furthermore, I don't see it making horrible mistakes if it can be set to "colonize closest, highest level planets first"... where it basically goes down the list of planet quality for planets in range, and then tries to colonize the closest, its definatly not a smart idea at the begining of the game, but in a HUGE map it can be a lifesaver... it would also need an option to turn off the rename popup to make things really simple... and a rudementry planet construction AI (ie, the ability to set it to autobuild a few core buildings on each planets before nagging you to fill in the rest)
The game already has a function to show all known non claimed planets and sort them by quality (which i use often, having an option to send closest colony ship to a planet from that menu would be a awesome... but anyways, this can be used by an algorithm that does the following:
1. filter out of range planets.
2. Find highest quality plenet. colonize the closest of that quality (so it would NOT go for a closer but lower quality planet).
This has the potential to cause SOME problems... but much less then colonizing hundreds of planets manually...
Do you even grasp the size of the largest galaxy? it is comprized of 18x18 sectors, each is 15x15 parsecs (aka, squares). Thats a grand total of 72,900 squares... almost 73 THOSANDS squares... this is huge and managing it is insane without some more automatation!