Stores that get enough complaints (from the right people) will probably cover a particular issue of any magazine.
That company policy they always refer to likely gives this discretion to district or regional managers.
It shuts the complainers up. The managers just want to sell groceries. They don’t care about anything else.
I read somewhere that people complained about the National Enquirer for political reasons but used the children seeing racy pics on it for an excuse to cover it up. As I was checking out someone asked why it is covered and I explained why. Politics. I said some people need pacifiers. The man ahead of me nodded. The clerks thought it was strange it had to be covered and did not know why.