From what I can tell, it's mostly functional differences.
Both the SE and the Core line will have dual outputs on the side of the guitar, so the player can split the piezo and magnetic signals to separate amps, or just run them through one output to a single amp/interface. The Core line has a mini-toggle on the top of the guitar that allows you to switch between magnetic, piezo or mixed outputs. The SE line does not have this, all switching between functions is done through the volume knobs.
Also, on the Core line, the outputs are "Mag/Mixed" and "Piezo" thus giving the Piezo it's own dedicated output. On the SE line, it's reversed as "Mag/Mixed" and "Mag" giving the magnetics it's own dedicated output. Not sure how or if this really changes much, but it is a different approach.
On the Core line piezo, you can adjust the individual string volumes with a tiny screw driver via a control section accessed through the battery port of the piezo board. There is no way to adjust the individual string volumes on the SE board (last I knew).
In terms of sound, I don't know if there is a whole lot of discernable difference....none that I've noticed through watching online videos, at least.
Those are the main differences that come to mind for me.