The mod generates a layout for me that can't be attached by the flying machine. There were 2 pumping, each completely surrounded by crying obsidian (link in the description).
But together with that fact, the efficiency of the farm aren't the correct number anymore. Because not all spots where the mod think they can be harvested, can actually get harvest.
There may be an algorithm that's prevents that from happening. They shut check if it would be may better to remove a butting amethyst to increase the spawn rate or placing something in there (buttons won't work) for preventing the amethyst growing.

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I'm aware of this shortcoming, it's on the TODO but I never got around to addressing it because lazy..