Yes it’s a little confusing because they’re both in the App Store, but MarginNote 3 is a revamp of MarginNote (Pro). It’s an independent developer, from what I can tell.
It is quite similar to LiquidText, but I think the two unique features are the ability to send straight to Evernote, and the way in which the mindmaps are made I think works better with extracted text. (Especially the ability to OCR extracted text, which as far as I last read up, LiquidText doesn’t do.
It’s a fine app though, so you can’t go wrong with LiquidText either.