Creating a low-cost pin-compatible Arduino/Due board using an STM32L471

that's what's in the PDF of the mega2560 schematic! damn it this sort of thing pisses me off: the reference design that arduino.cc released (the actual eagle files) are hopelessly out-of-date.

When and where did you get your copy? The versions I see now at https://store.arduino.cc/usa/arduino-mega-2560-rev3 look updated and current.

uncertain about what (low-er cost) single-channel op-amp to put in its place?

LMV321 ? Seems to be available from several vendors, and on ali-express for cheap. Beware the non-V version, which isn't a rail-to-rail-y.