It was interesting to hear that Moon Music turned into something bigger than they were planning at first. It probably means that at some point they realised they have written some really good material, which made them work longer and harder to turn it into a big proper album. And if the story about Brian Eno being involved is true as well, then wow! Exciting!
They always record more than they need and through process just realise some material is stronger. In case of Aeterna, not sure if it even deserved to be on album. I never got the big hype, yeah it's a nice moment in a context of show, but otherwise not that strong track from start to finish. I think B-sides are just a way to give fans something more and special and it's nice they want to release them again. About MOTS3, it seems like if there is something to be called MOTS3 then it could be the musical.