The abstract problem absolutely has legitimate interpretations outside of phylogenetics, and there are other ways to formulate the problem that directly relate to linear algebra over GF(2). Reformulating the problem in those contexts also failed. It is a legitimate, pure CS theory question, that itself relates quite closely so several other known results including in computational geometry

https://arxiv.org/abs/2003.02801

https://doi.org/10.1016/j.comgeo.2024.102102

https://arxiv.org/abs/2107.10339

https://dl.acm.org/doi/10.1145/1998196.1998218 — DOI: 10.1145/1998196.1998218

The problem in the post is right at the edge of variants that are known to be in P and variants that have been proven NP-complete. So, in this case, it is simply Fable refusing to engage with a theory question.

Also, as I note in the post:

This may not be true for everyone, but for anyone working in Bioinformatics, Genomics, Computational Biology, Biology, Cybersecurity, and, seemingly Computer Science, this seems to be the case.

Of course it can go on a tear for various coding challenges. However, the more that I learn the more that I also suspect that it rejects not just prompts that may relate tenuously to biology or cybersecurity, but also otherwise completely innocuous prompts that are issued by people who work in areas adjacent to biology and cybersecurity. If true, I think that is certainly a bridge too far, and a hard policy to defend.