Looks amazing! I just opened my pledge so I'm not quite at the make your own board level yet. I haven't read the rules yet but how does the game handle large creatures trying to get down in the cracks? If they're bases don't fit, they can't go in there?
Better read the rules then.
There is nothing in the rules that supports your assumption.
There are rules for how many units can go on each space and how the special terrain rules work.