Hello campbell. I'm glad you're coming back with your questions. Alarm bells go off when I hear 'silicone' on the AirForums. Let's back up a little...
You could tell us what type and year Airstream you have -- or change your profile to include that info in your User Control Panel (User CP) at the top left of any forums window when you are signed in. This may bring responses particular to that year and model.
I can guess that you are talking about the storage area between the lower back shell and the bumper. Yes, this is a common area for breakdown of seal and potentially some frame flexing to open up a path for water (the frame is more flexible than the rigid shell). Is this the area you are talking about?
As a starting point I must say that silicone must never be used against aluminum. The oxide on the surface of any aluminum may decide to stick to silicone caulk with a passion, while an inch to the side the oxide prevents bonding and allows water passage like a river bed. It is important to use other caulks like Sikaflex 221 or Vulkem. Use the search function to find out more.
Let us know your year, length and model of Airstream. I think that it is necessary to understand the condition of your plywood floor and the frame underneath. Hopefully we'll get some responses ... please give us more info.
[on edit: How did I miss you saying '64 Ambassador? It never has to be said if you put it in your profile anyway. Sorry.
At least that's not the late '70s period of rear end separation, although frames weren't as hefty back then. Still could be a floor issue. Do you see any caulk at the shell-bumper-hatch junction?]