Misery's End chose to be with Repose, so Serenity gave it to Repose, who'd later assemble all the other seven artifacts of Usagi Tsukikage.
LSR lets you play as Shinica, which... is just a dream she had. A very silly dream, though! She'd play differently. Instead of Ataraxis, she'd fight two clones (no, Narvelysica isn't there, and Tyamitica takes Tranquility's place).
LS + LSR + LSM? There's a bundled idea! But... what about Ilina? She'll just be sitting on her bed, playing the trilogy (as created by Lunadine Crimstaine) probably.
So in other words, Serenity gave up the best weapon in Lunar Shadow and in the long run got a better deal out of it? Good for her. Also if Lunar Shadow Reverse (which sounds like a Mirror Mode kinda deal) is non-canonical, then surely having Shinica fight Ataraxis wouldn't mess up the LSP canon would it?