From the sounds of it, it had to have been an alternate universe, or else there was more to the Flamel story than Hermione had realized. The Philosopher's Stone as she'd known it had only been in existence for a few hundred years, not thousands. And she still wasn't sure what was meant by a "Divine Source." As for this whole Trinity business....

"What sort of people were involved in this Trinity organization? And are they known by any other names?" She hesitated for a moment before positing, "Death Eaters, perhaps?"

It was unlikely, but where one common thread existed, perhaps there would be others.