Xion seems to have been there long enough to make for the restoration of Sora's Memories take about a year.
I also doubt Roxas left that far after Xion "took her leave".
She'd have been there long enough.
I'm still having trouble believing she was around long enough to call for one, particularly because it's marked with both Oathkeeper and Oblivion and (at least right now) there's no evidence to suggest that either of them were aware of those, nor that Xemnas had any reason to believe Roxas would be wielding them in the future.
We're also still pretty unclear on just how long she was around. While she seems to have an affect on Sora's memories, Roxas does, too, and it's possible they collected Xion (or whatever happened to her) and then had to pull teeth for a couple months just to get Roxas, too. Admittedly, the models are all aged to circa KH2 because the progression of time in KH is notoriously wonky, but it makes more sense to me that she would leave prior to the Proof getting established.
This is a possibility, but I could also definitely see Nomura having her Proof in one little room off to one side that we didn't get to enter in KH2 because Xemnas destroyed it afterwards. For that matter, where's Xemnas's Proof? Of all the Nobodies, you'd think he'd want one the most. Is it possible hers was with him, if she was Experiment No. 1 with ties to Aqua?
Was there even room for a ledge, and why put it there?
I totally forgot about this--if I'm assuming, Rain, shut me up, but this immediately makes me think of Kairi's princess coffin. It was way up away from all the others and you almost had to look for it just to obtain the Oblivion in KH1. If Xion's were set up like that, that'd make for some healthy parallelism--considering the love affair with parallelism that persists all through KH2.