In a normal wind area the 10ft with rectangular magnets seems fine but in a higher wind area you really must make sure it does genuinely furl at about 500W.
You may be able to increase the disc diameter a bit and get the #16 wire in with 12 poles, a few turns less wouldn't hurt as you will most likely end up increasing air gap on a 48v machine.
Going to 16 magnets will give you something more rugged and more like the round magnet version. If you do this then reduce coil turns so that you don't cut in any lower speed than the original winding. You will need larger discs but you should have room for even thicker wire than #16.
If you have the #16 then use it and it will be fine. Be prepared to have to add some line resistance as I think it will stall fairly hard.
It will be a more robust winding than the 12 pole with #17 wire but still you must make sure it will furl safely. peaks to 1kW should be ok but 600W sustained for significant periods is all you can expect without compromising reliability.
Whatever you do if it furls correctly it will be ok, if not you will have trouble in the first real storm.
Flux