"Only one thing is certain - those who return are changed beyond all recognition."
"The warrior who came down the mountain looked the same as the one who had climbed it, "
-http://na.leagueoflegends.com/en/site/mount-targon/leona.html
So if Leona looks the same, how can she be "changed beyond all recognition"?
I know it's figurative language, but still =)
As you said, "beyond all recognition" is figurative language. Pantheon came down from the mountain and looks the same as Arteus, but he is unrecognizable by the fact that he no longer is Arteus
Leona and Diana inherited aspects of the sun and moon respectively, but only a sliver of an amount. That's why they still retain their personalities. What they were given however was ancient memories and knowledge from these aspects. Pantheon, being the aspect of war, also has an arrogant streak about him, therefore he'd consider it a privilege to take everything that Atreus was and use him as a mortal host.
For whatever reason, Diana and Leona are supposed to be exceptions to the rule.
"Beyond all recognition" refers to her old lore compared to her new lore.
