It'll work, but it's probably not the easiest, quickest, or safest way. Also, keep in mind that heating the hell out of those bottles will reduce their overall life span. If you're only going to reuse them once or twice, it's not an issue. If you want them to last almost forever, boiling or baking is not the way to go.
My method is to clean and delabel (two birds, one stone) by filling up the bathtub with warm water and Oxiclean. After a few hours of soaking, I store the bottles until I'm ready to use them. When the time comes, I give them a quick rinse in tap water, and hit them up with a
vinator/sulfiter filled with water/Star San mix. Cleaning takes a few hours of soaking, which is fine because I'm delabeling at the same time. Santizing takes maybe 3 minutes for a 5 gallon batch worth of bottles.