Once the images are uploaded to the UGC server, they can be served up with any standard Image Serving Command. Here's a link to the fmt parameter which supports transparency, http://microsite.omniture.com/t2/help/en_US/s7/is_ir_api/#fmt
Here's an example UGC request serving a transparent image, http://s7w2p1.scene7.com/is/image/TechSupport/ugc/328883369.tif?fmt=png-alpha