The AutoConquer patch is designed to assist the AI in the later game stages when it comes to taking new planets. Investigation has revealed that as the game progresses, the AI has a harder and harder time fielding Transports properly, resulting in excess planet bombardment, which is an inefficient advancement system. The player, on the other hand, doesn't suffer from that problem, giving them an expansion advantage.
The way the patch functions is by changing the Planet Destroyer weapon class to Planet Conqueror. In the default game, if any AI ship that takes part in combat has a Planet Destroyer weapon, then it will automatically get used, completely destroying the planet (by default, only the Stellar Converter has Planet Destroying capablities). Once the patch is installed, the same system will occur, except instead of destroying the planet, the aggressive empire will take it over completely intact. The planet suffers no damage whatsoever.
As mentioned previously, only the Stellar Converter is considered a Planet Destroying weapon by default - and as a level 50 (roughly) tech, it is rarely researched. For this patch to be effective, other weapons will need to be designated as Planet Destroying. The tag for this is PntDisWp=1. Note, for a weapon to be considered Planet Destroying, both the weapon itself and the weapon mount must contain the tag. By default, all Spinal Mounts and Heavy Weapon Mounts have the tag.
Note: Although the original purpose of this patch was to help the AI in the later stages of the game, some players have chose to use it to complete replace ground combat by giving all beam weapons the PntDisWp=1 tag. This works, and can lead to a completely different strategical game. However, it should be mentioned that the AI is unaware that it can conquer planets in this fashion, so it will not be playing in that fashion. This gives the player the advantage in the early game.
Also worth noting is the fact that the Sitrep does not currently report that the planet was conquered. Hopefully a future version will rectify this.