Good way to handle structure on terrain

I'm trying to figure out the best way to handle a structure I'm working on when it comes to terrain, my structure is a very large tree, and in most cases using terrain_matching is... okay, however extreme terrain does weird things of course, and it will generate floating on top of water rather than following the ground underneath, so is there any better ways to handle the generation of a structure like this? the base of the tree is a bunch of roots which cover an area of roughly 32x32.