Aside from Roland technology, Graph Tech makes the Ghost system which - depending on the model - can provide MIDI or acoustic piezo individual pickups embedded in the guitar saddle. Godin does a lot with Ghost saddles for their MIDI guitars. The Ghost system is the only MIDI pickup solution that offers an invisible look to it. Fishman's TriplePlay also offers this functionality, but it isn't a built-in interface.
As digital pedals get better I'm sure we'll eventually be able to get away without a MIDI pickup, but I'd bet overtones inside some chords could really confuse a system which is effectively trying to decode frequencies in real time to identify the fundamental. However, with that said, Digitech is getting really close with this ability in their long-running Whammy pedals to transpose entire chords as well as individual notes.
As digital pedals get better I'm sure we'll eventually be able to get away without a MIDI pickup, but I'd bet overtones inside some chords could really confuse a system which is effectively trying to decode frequencies in real time to identify the fundamental. However, with that said, Digitech is getting really close with this ability in their long-running Whammy pedals to transpose entire chords as well as individual notes.