There is a big gap between what I understood the article to say and what you are theorizing. The article discusses changes to the egg or foetus (one generation) not a permanent change to the genome, as I understood the article. I’m sure there are positive effects and negative effects to the changes (I would picture a child being born into a stressful environment as needing more aggression, intelligence, and a physical strength . . . perhaps at the cost of longetivity, ability to relax, and that sort of thing). Which sort of person would you want to be? I can’t choose so I’ll trust God to have set it up right.
Agree with comment about God setting people up the way they were supposed to be born. However, if God gives up the ability to change that, then might that be God's will, too? For instance, many people are born on the bottom rung of the socio-economic ladder, and yet they could conceivably climb that ladder and end up on the highest rung, with their children being born into that level. Was God's will for those people to stick on the bottom level? Although they were born into that status, obviously not. Already, the epigenome has been altered by scientists methylating parts.
As for intergenerational effects, the article mentions starving Swedish grandfathers affecting their grandchildren's longevity. That's two generations right there. Furthermore, if parent '1' affects the epigenome of child '2' for that child's entire life, then child '3''s epigenome could be affected, too. And then child '4', '5', etc. Suspect that if that is the case, then the affects would weaken with each generation, but still have some affect on the epigenome for generations. A hypothesis to be sure, but not too much of a stretch.
Studies in mice have found some of these effects lasting at least 2 generations after the one in which the mother had certain environmental effects.
Is epigenetics is the explanation for why societies that experience severe famine remain below average in height for several generations after recovering normal nutrition? I believe this phenomenon has been observed repeatedly in history.