I have performed DNA studies in my career. Measuring and interpreting methylation - understanding what it is, why, when and where it is present is at its infancy at best.
Sadly I have prime view how clickbaity ideas like this one drive most of the motivations behind investigations in life sciences.
It is not just this paper that is bullshit, the whole field of "epigenetics" that this paper is a representation of is bullshit as well - this paper is just one out of the long line.
As I pointed out it there is simply no proof that handling changes DNA. It could just as well handling stimulates the development rate which, in turn, also shows up as another signal.
The lie is not that A and B are present at the same time. The lie is presenting story as if A was caused by B. There is absolutely no evidence for that.
Now hundreds of scientists want a piece of the "cool" story, will jump headfirst into proving how LOVE will reflect in the DNA. No one will care about understanding what the heck is methylation - they will all be chasing baby handling and methylation. That's what I have seen happening and will keep happening thanks to papers like this.