Even holding in the endzone, on a pass play, according to the rule mentioned above, would not be a safety because it isn't a spot foul.
The only spot fould that comes to mind quickly, for my age anyway, is intentional grounding.
Not that it's correct, but I swear I have heard reference to holding on pass play = safety.
I believe that it has even been called and awarded that way too. Maybe it is different, but I doubt it. I'm guessing that the holding just wasn't in the end zone on this particular play.