Before running each instance of WoW, Keyclone modifies each config.wtf to set the WoW client window size to the same size as the maximizer region it will reside in.

But, if config.wtf contains a window size smaller than 800 horizontally or 600 vertically, WoW will reject this and default back to 800x600 when the game runs. 720x450 in config.wtf isn't allowed.

What you need is some way to prevent Keyclone from modifying your config.wtf files, perhaps make them read-only, and manually set them to 1440x900 yourself. When the windows get resized, they'll retain the correct aspect.

I don't know how keyclone will handle being unable to write to the config.wtf files.