Cyclotomic polynomials are incredibly standard in the field. The only researcher I know of who has issues with them is DJB, and there has not been significant advances in cryptanalysis due to usage of cyclotomics (with the exception of problems not used by NIST candidates, meaning the whole SOLIQUAY thing)

My understanding is that he worked on NTRU Prime, which would have somehow benefited from NTRU being choosen.

NTRU also relies on cyclotomic rings, so if distrust in cyclotomics was a good reason to reject Kyber, it would apply to NTRU too.