It does seem to work very well in stopping rust. Its even good on battery trays because it can resist the battery acid. One of the best resources on how to use POR-15 is the information found on the web site itself - just look through the links.
For a fender bubble I would say it would do well, provided you can work to treat/paint both the inside and outside surfaces. In most cases a rust bubble is going to progress from the inside out, so by the time you see it the metal is pretty thin.
On the 240D I have rust bubbles that have popped.
Ken300D