Sorry for the possible plug I am about to do, just figured it'd be good to let ppl know.
I made two small patches with this mod in mind specifically, and for those who don't want Lush
planets to be cluttered with unneeded structures while also allowing other things to spawn.

To remove both the Mineshafts and Gates, use this:
https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=3468514615
If you want to remove Gates only, use this:
https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=3468546478
Make sure to use only one, not both.
Nothing crazy should happen if you have both afaik.
But it'd just make one of the mods redundant,
as both of them do generally the same thing.