I checked out Wallpaper Engine and it seems pretty cool! From what I read, the application feature is Unity based so maybe its possible to just open the .exe through Wallpaper Engine's task-bar menu. If that doesn't work, I think I would need to make a special build that doesn't use the initial resolution dialogue at launch. Give it a try and see :) I'm not so sure I have enough time to create new builds of Poke Abby these days so I can only offer verbal support for the time being :p
And to answer your side note question; there is no extra content in the HD version of Poke Abby. It's purely an up-rez of the character models. Later on down the line I may further update the visuals but I don't think I'll be adding any more content to that game unfortunately.