Hemi,
My money is on option 2, I'm afraid. It's the more expensive option, but you don't lose any capacity in the CT (OK, you lose 1L, I'm sure you can deal with it) and you get your fridge in the CT. As Dan says, I'm a fan of seperate units vs a single combo one.
As far as a unit that functions as a proper fridge/freezer, I think National Luna do one with proper seperate compartments with each having it's own temp control.
Probably not cheap, and the freezer compartments on the ones I've seen have been pretty small, which might be no good for you. I'd say definately not cheap, but this new model might suit you :
http://www.nationalluna.com/NLR90.htm. 50L fridge compartment, 40L freezer compartment. Seperate thermostat for each compartment, the duck's guts.
If you want to go this way, it might be worth talking to someone like EvaKool or Trailblaza (Norcoast) - they might be able to build you a unit with seperate temp control and circuits for each compartment.
But your Option 2 above is probably going to be cheaper than that, especially if you sell the Engle to fund the 2 x Waecos.
EDIT - GetAWaeco currently have 2 x CF35's left as seconds - $745ea :
http://getawaeco.com.au/default.asp?id=416&catId=6 .
I've found myself wanting to pick up a little Waeco to use as a seperate freezer myself. Would come in handy.
Good luck!
Matto