Hi Jacobus... maybe a pic of the mesh too would help?

In your first pic, looks like long thin tris are creating artifacts?

The technique I've found, that seems to help for making a circular boolean into a plane, is simply to reduce the area around the circle.

So for that small circular topmost window, I'd break up the mesh plane it is being inserted into, so that the circle is being boolean'd into a smaller square, with the edges of that square being just a little longer than the diameter of the circle... if that makes sense?

It looks like that section of wall that the small top circular window sits in might just be one big triangle at the top there, in your mesh? Would that be right?