not to criticize your design, but 4 font and 3 atlas references seems a bit high. Are those references just for different resolutions or are they actually being used in your UI? if they are just the different resolutions, then you should only have one atlas reference and have all of your ui components using that one, and one font reference where all fonts are using that one. Then you should only have to clear out those two reference objects before building.
If you have 4 fonts and 3 separate atlases in your UI, then I would seriously recommend redesigning your UI to stream line down to one of each. each atlas requires a draw call and extra memory usage, so I would do my best to minimize the need for extra atlases and fonts, especially if you are wanting to run well on older devices (3gs and lower, most android phones).
As far as automation, I am not intimately familiar with tweaking Unity's build process. My first thought would be to write a standard Editor script that would let you just push a button and clear those references before firing off a build. I am not really sure how to make that whole process completely automated.