Yeah, I did a little experimenting before I put up the rear wall. I could cut some excess silicone off the deck with a razor blade, but the dremel easily took silicone, paint, and primer off all the way to bare metal in a blink of an eye. I decided just cutting off the excess blobs with a razor was enough, and I'll just fill the gap with PL as you suggest.
On the bright side, I now have a rear wall (minus a door)! I also cut and installed one interior wall's worth of styrofoam insulation. Looks good!
I have my eye on a cragslist post selling 10, 4x10 sheets of 0.040 aluminum. These are seconds (with a few dings and rough edges), but they might do the trick. I will see how they look and post what happens.
I have two quotes from local metal shops for about $90 a sheet for that size, whereas the craigslist seller wants $35 a sheet. At that price I could get a few extra sheets and work around the imperfections.