It's kind of by design, in that in Opus 13 we removed the older "hacky" method we were using to keep the progress dialog on top of the Lister that launched it. It's now a standard "owned" window, which means it always appears on top of the Lister. One side effect is that the Lister always comes to the front when it does.
We've improved this in 13.7.5 - the first time you minimize the progress dialog to the taskbar, the link between it and its parent Lister is broken, so when you restore the dialog it'll no longer bring the Lister to the front with it.