As I understand it, the current settings for Trees do not look at the placements of Foundations & Walls, they just clear them from within a radius around the center of the base spawn and put them back when the base despawns.
"Eject Tree Radius When Spawning Base": 0.0,
"Delete Tree Radius When Spawning Base": 0.0,
"Respawn Deleted Trees When Despawning Base": true,Could you look into updating the mod to only remove Trees that are withn the bounding boxed of Foundations & Walls?