Recently, I tried to conquer a minor race (The Andians I believe) and I went to attack their defending ship on the planet, and instead of attacking, I went straight to a planetary invasion. (I had a transport in my attack fleet to escort him.) Beyond the fact that I completely got around the defenses without even a fight, I never got to choose what kind of planetary invasion tactic I was going to use. It just set me up in a traditional invasion against the Andians population. I lost, so I can’t tell you what would happen if you managed to take their planet while the enemy ship was still in orbit though.
I was running version 1.0X01. (The newest version)