So I've recently added in flybys of enemy ships, after a few tests I've decided to just have them launch missiles at you. The RPG has been replaced with a voxel model of my own design, however the underexplosion of the original needs to be changed/removed.
Tricks had to be done to get the ships' shadows to properly show on the surface, in the Build engine the floor position of shadows is set on creation, so it doesn't show on certain heights. Luckily this is minimized by the large mostly flat area they fly over.
I think they should be firing more missiles...perhaps I can link that with game difficulty.