I'm not exactly sure how collision damage is calculated. I guess it uses a callback from bullet, so if there is collision damage, then there was indeed a collision with the planet. There should be no difference if you activate collision damage. But maybe 1337 is right and collisions are sometimes triggered too early because the simulation is unstable? Without collision damage you may not notice it because it's only for a single tick... but that's just a guess, no clue.
About projectiles: I think the collision radius of projectiles is greater than the radius of the projectile itself. This is often intended to make it easier to hit enemies. However it might be a bit too large for some projectiles... this could be adjusted.
@Planet size and projectiles: Projectiles don't have to bounce from the planet's surface. In fact projectiles are not even real physical objects, they are ghost objects which don't collide with other objecst. Instead they only receive a callback from bullet. No one cares if this callback is a little too early or too late if you hit a planet.
Also collision with planets is not even really needed for ships. If you allow a player to fly that close to a planet until he smacks his forehead on the planet's surface, you have a problem anyway. Instead we should apply some damage if you enter the atmosphere, issue a warning, and finally destroy the ship if it gets too close. At least that's how I experienced it in other games. We could do it differently of course.