Well I'm obviously NOT Khaled so I don't know how he designed things, but if I have a window set as maximized. Then I open it with -n that will change it to minimized.

Try it with the basic window command. /window -n @window. Regardless of what I had this window saved as, I now have made the window set as minimized. Just the same as if I decided to open it this time with an edit box. (window -e @window) and before it had none. I changed the settings with a command vs. the popup.

I don't see a bug, I see a conflict of interests. You want to open the window minimized yet you dont want the window minimized. Maybe a join switch that doesnt make the new window pop up on top. i.e.: an added feature request vs. a bug.