To close the loop on this - no issues whatsoever using the DNIe at the e-gates, both departing and returning. Not sure what would've happened if I got sent to a passport officer (not that I was doing anything wrong, but they likely would've asked how I planned to enter on the other side, opening a can of - legally acceptable - worms).

Just a side note - you need to place the DNI photo-side-up on the scanner (chip against the scanner) rather than the other way around. Panicked a little at the start as I kept getting dinged until the auxiliar helped me out!