I'm also happy to see transparency supported in LR4.4, but the only output that is usable is 'Export' or 'Edit In.' The Book, Slideshow, Print, and Web modules all output transparent areas in gray color.
For now one option is to create a "flattened" copy of transparent images with LR adjustments applied using 'Export' or 'Edit In,' and then use those images in the other LR4.4 modules.
I also vote to add a Preference selction to show transparency as gray, white or checkerboard. But all "flattened" output from the Book, Slideshow, Print, and Web modules should render transparency as white – the same as all other applications.