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Well, the Builder is much faster by default, and much easier to add fortune, but the Ender Quarry is MUCH more energy-efficient. Plus it doesn't leave a world-hole. This, however, does not account for that fact that the builder can blacklist (I think it can whitelist too) certain blocks. I forget if that just means that it voids them, but it may not mine them. Really, it's up to you. But, if you ask me, the Ender Quarry is much more practical, but the Builder is better all-around, plus it can do more than mining.
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