I would think using a single array would be best and just change the X coordinate to reference the biome or what-not. Multiple arrays mean more objects being loaded.
I tend to use a single array and set the dimensions and references as needed without any noticeable drop in performance... unless you're talking 100s of dimensions.
Maybe the memory management of C2 and arrays works differently, so I'm just guessing.
Alternatively, you could use a single array, store the array in the Dictionary, and clear the array for a new biome.