Okay, let me try to decode what you said.
1. In full screen the icons don't match the hitboxes
In settings have you matched full screen to your monitors resolution? (ex: 2018x940)
2. Supernovae cause your game to be unplayable
There's a simple fix for this, avoid supernovae, they aren't really that good at the moment and in my opinion don't add much to the game at the moment