Meh. This strikes me as a word salad (Methylation! Neanderthals!) of untestable hypothesis.
Dysmorphic body features are pretty common in modern man, but generally these are actual heritable mutations or chromosomal aberrations that might make people sterile. If methylation caused dysmorphism, we'd be studying it. BTW I once saw a teenage girl in a wheelchair who had birth defects, and she had amazing cave man brow ridges.
Probably the real role of methylation is seen in mental illness. Adverse conditions effect the development of the young brain at the level of methylation, and this persists for life and probably into subsequent generations.