First, I want to hilight I completely understand the desired design behavior of Alt+tab being application switching while alt+~ beeing the per-application window switch.
I have also read https://bugzilla.gnome.org/show_bug.cgi?id=69748.

However, I think there is an inconsistent behavior when you want to only raise the last focused window of an application:
1. Press Alt+Tab until the switcher is visible and you go to the hilight the desired multi-window application. Keep alt pressed
2. a) if you press the down arrow key, the first window of that application is hilighted and you can raise only that instance if desired
   b) if you press key-above-tab (² or ~, depending on your keyboard configuration), however the second window of that application is hilighted, so you need to cycle back all the way down to first one to only raise that one.

I suggest that when the switcher is displayed, after an alt-tab with alt keep being pressed, the first key-above-tab press hilight the first window instead of the second (as if you pressed the down arrow key)

I'm happy to provide a patch for this if what I'm telling make sense to you.