Why is my baked lighting so messed up?

Uhm… let me correct this…

Instanced static meshes are not “welding” the meshes together. All instancing does is it tells the CPU, “This is the template for the mesh I want to draw, and I want to draw a thousand of them!” and then GPU will then use its massive parallelized processing power and draw the same mesh a thousand times, all in ONE draw call. If you have a thousand static meshes, which all happen to be the same static mesh and you don’t use instancing, then you’re going to have 1,000 draw calls instead of 1. Instancing is great for batching up draw calls on things which there are a lot of. I’m sure that behind the scenes, the foliage tool takes full advantage of instancing.

I think what you’re trying to recommend is ‘welding’ the meshes together so that the GPU treats them as a seamless mesh. I’ll look into that and give it a try. I think auto-welding might be enabled by default though.