This issue persists in UE 4.19.2-4033788
edit: It does work if you specify the same resolution as specified in-game via the r.SetRes console command. If one does not specify a -WinX and -WinY, or if one specifies a different resolution, the resolution change will trigger the window to be reset to the centre of the screen.
This is therefore not a problem if one is using a fixed resolution. For myself however, I am developing an app to run on a whole host of different resolutions (from 1280x720 to 5120x2880). I have made a function to detect the native desktop resolution (or scaled in the case of 4k or 5k monitors), and I then r.SetRes to approx. 2/3 of the height of the screen (or closest 9:16 resolution). As such, having a fixed resolution is not an option for me.