Thanks to Cloud and Cid's cooperation to change Meteor's trajectory away from his villa, during the altered ending, RedXIII makes an assessment of the situation.

"Forget Yuffie's house and the ninja assassins. We gotta worry about the Planet."

I could imagine that terrible music playing while it shows Meteor destroying Yuffie's House instead of Midgar.

When the Staff Role starts, Cloud turns to everyone and says, "Well, let's celebrate the survival of my precious villa by having a party over there!"
"Yeah, man. Let's all do our levah fo' limit breaks at the talent show. I'll do Catastrophe!"
"Hmm, maybe we should skip that one, Barret."

500 years later

Red XIII shows his kids the ruins of Yuffie's House.