I don't know much about creating apps, but would it be a solution to have an 'export' button that makes a checkerboard alpha transparency layer that automatically activates underneath all the other layers at 100% opacity, then you click on a 'save as' button which opens the file directory to save as png, bmp etc?
I'm only new to this whole coding thing so I don't know what's easier/harder depending on what language you're using and what lines of code you'd have to change.