But either case we talk about commercial products. The games are still copyrighted commodities to be sold. I assume they get licensed by the copyright holders to update them and sell them in gog. I do not see how a "charity"-based process would make sense or be honest here.

What are you talking about? Charities can sell products, they're just not supposed to make a profit, so all profits would have to go back into preservation.

I mean we can go off on a tangent about why IKEA should not get away with being registered as a charity, but as long as GoG is not doing tax evasion I don't see the problem.

The copyright holders still make profit from the sales as for-profit entities. I do agree that non-profit status would make more sense for the preservation program though. But it still would not mean that nobody makes profit out of the result.