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"Because they didn't already have enough to point to as it is?"
The elephant in the room is that in the grand scheme of things Nintendo is objectively pretty lazy about enforcing their IP protections. For every AM2R, there are literally hundreds of Metroid fanworks that they leave alone on account of no one actually caring about them.
They make a big production about vigorously making an example of the high-profile ones so that they do not actually have to waste the resources dealing with the no-profile ones.
Same principle as being in prison or a substitute teacher at an elementary school.