Stop Mail Activity window being always on top in El Capitan?
I had a conversation with Apple Tech Support yesterday regarding this issue, which I also find frustrating.

The answers I got simply deepened and widened my frustration. This behavior was a conscious decision on the part of the programmers. The logic went something like this.  The Activity window is a diagnostic therefore if someone wants to view it, they will want to view it in front of other windows anyway. They kindly left us with a Command+0 option to toggle its display on and off.

I let them know that there are various functions that I use as diagnostics and I like to keep them where I can see them at a glance but where they do not interfere with my work. I let them know that I have always had the option to toggle the display on and off and that I also have always had the option to see the window in front of all others, all I had to do is click in it and it immediately came forward.  What they did is to make a decision on my behalf that reduced my options and that is a way of thinking that I don't appreciate.  If they want to give me more options, that is fine but a decision to reduce options is usually a poorly thought out decision.

I am still looking for a solution through the terminal that might allow me to regain my previous functionality.  They were not forthcoming in this area.  They simply said that at this point, we cannot do it. Not a very good answer, certainly not the one I wanted to hear but I suppose having the answer, like it or not, is helpful in a way.  Now I can dismiss the thought that it was an accident and decide how much time I want to invest in working around their poor thinking.