Not sure if this was addressed in v1.3, but when I get the "council gives a new planet to someone" event, and I recieve the new planet, and my alignment is neutral, the new tiles aren't upgraded automatically. If I take a planet from someone by force or colonize a new one, however, the bonus is applied automatically in most cases.

The other problem I encountered shortly after (because new planet was in enemy territory) was that the planet revolted, but I could still access it in my list and zoom into planet view. This might be a known bug, but it's revealing when it happens on the dreadlords campaign as to how they build their colonies