You may use multiple RTD devices with our MAX14778 beyond the rails multiplexer as the resistance of the mux is only about 1.5 Ohms but is very flat and matched between channels.
This way an initial calibration (in your micro) will ensure that multiple PT100/1000s track each other exactly.
This has been proven in an aviation application where multiple RTDs were used on a wing control surface.
A typical configuration would be: