Is it wrong to overlap mesh? Or should everything have a boolean?
For example… I am building a treehouse… In the image, you can see some of the wall in the corner of the tree through the trees mesh.
Should I bool this? or is it ok to just leave as is?
I can’t see well what you have there, but I think it should be fine, you may have rocks overlapng the terrain for example. Everything that is a separate object irl you might want to keep it separate, also easier to make changes later.
OK thank you! That helps. 
It’s not a lot that is crossing the trees mesh, but since it is still crossing that mesh, I was concerned about issues with baking textures with the overlap.
Thanks again 
Ahh, I see, baking might be a problem, I haven’t baked many things but iirc you have to select the high and low poly meshes, you might want to join both objects into one (not boolean) or to the same collection, I haven’t done any baking since 2.9 series started so I’m talking from memory.
I am not close enough for any type of baking, I am still in the concept stages of this… I am just trying to prevent problems as I create and not after trying to fix things. If that makes sense.
As so often, it depends. Mostly on the purpose of your model.
Overlapping meshes are not necessarily a problem if you just make still renders (well, they can be a problem if you don’t just have overlap, but co-planar faces on surfaces, because then your renderer will have issues deciding which polygon is in front, and you’ll get something called z-fighting). If you ever see faces all black in Cycles that shouldn’t be, that’s likely your problem. You can also get odd shading with overlaps, but if speed matters, I might not bother unless there obviously is an issue.
Overlapping meshes are a big problem if, for example, you want to 3D print your objects – you can’t have that. They’re a problem for exporting assets to game engines. When animating, you also want clean topology. When downloading objects from various 3D sites, I really hate getting one with overlaps all over the place which I then have to clean up myself, so I’m pretty determined to only share models with clean topology.
So I’d think ahead about whether I might want to use this model in other contexts, and adjust my modeling accordingly (you don’t necessarily need to boolean things either; you could just snap them together).