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Steve, a panel with a shadow on it is simply crippled. You're better off doing an installation that won't have shadow problems. Effectively...if you lose 50% output you're going to pay double for your panel, and they aren't cheap to start with, right?
You'll also lose about 10% of power for every 15 degrees that the panel is not angled at the sun. i.e., if the panle is hanging flat on the stanchions and the sun is overhead, it is off by 90 degrees...and water reflections or not, that means you are about 60% down from full power.
So you are right to be planning ahead for the best possible mounting, it is time and money well spent. You might want to take a look at solarstik.com not that I would recommend it for a 31' boat, but to look at the concept. Mounting the panel(s) on a pole that gets them outboard of a stern quarter could be a good solution. They're out of the way, and the primary drawbacks are making sure you don't lose anything overboard, and of course, robust installation. A "radar pole" and a way to mount the panel could be a reasonable compromise though.