Interesting theory! I've never thought about the idea that the box somehow "contains" the Dandelions, but I think it holds some merit.
After recently beating KH3 on critical, I was paying closer attentions to scenes than on my first playthrough now that I had some context. One thing I noted was the scene when Luxord mentioned the box contains "hope", like you said. A few scenes after that, Sora says something to the effect that "hearts are hope". This reminded me of another theory floating around that the box somehow contains MoM's heart, which is what's going to allow him to return. But containing the Dandelions "hearts" through some data-copy or something would also make sense regarding that connection.
I'm very excited for the future of the series, hopefully the months leading up to E3 will have KHUx updates with some more clarification on where the story is heading, along with the upcoming DLC.