The second idea seems like the best bet. If you think your door panel will be able to hold the weight of the speaker and baffle, which I think it should, then you should be fine with mounting it to the panel and not the actual metal. I doubt you would have trouble with cancellation, even if you mounted it to the actual metal it would still act like a leaky infinite baffle setup.

Here's another idea. Have you ever thought about doing kick panels? If you're going to fiberglass anyways, kick panels are probably going to be about as easy as the door pod idea, but usually are much better with imaging. Only problem you could run into with this is if the car is a stick, then the clutch pedal may get in the way. What car is this going in? I may be able to find another idea for you.