Cubase can only mixdown to an output file, and then places it on new track, a new project, or can open an external editor. So Cubase is going to put it in a new track at the bottom of your track list.
So I think you already sorted it as much as you can, and the answer to your question about how “to mixdown onto existing tracks & w/o first deleting the tracks” is, you have to do the extra work, or make a macro.
Check out the commands “Find Selected in Pool” (works on multiple selected audio events in the project page), “Remove Unused Media” and “Empty Trash” At least you can automate part of this.