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The 5 gigapixel limit is always there for Full 3D processing since it requires so much more processing power to get it done. If you need to process more data with the Full 3D setting you can downscale your images a bit in Step 2 of the uploader. The limit is in megapixels, not megabytes. 5000 megapixels is 250 20 megapixel images. You can do up to 500 with .5 downscaling since that is also 5000 megapixels worth of imagery.
In general, Full 3D processing is meant for processing a single structure or object, not a big wide area, which is another reason for the limitation.
That being said, unless you are actually trying to render a building or something there are few cases where you would actually need the Full 3D processing. The regular processing creates 3D results that meet most needs (they are just less complicated).