Giving the thermistors a dedicated ground and returning it via a dedicated pin to the Due probably is the only real way to get good resolution on the thermistors. A work around would be to send the local thermistor ground back to the Due as a signal, read it, and do the math. That (of course) only works if it's a positive voltage ....
The converse of that is indeed to have a solid ground on the FD, so you don't put a lot of offset onto the Due ground.
The converse of that is indeed to have a solid ground on the FD, so you don't put a lot of offset onto the Due ground.