Voltage divider : using board voltage vs Power supply
The input impedance of an ADC with an analog mux can be pretty low. Typical microcontrollers recommend a source impedance no more than tens of kilohms. Changing R1 to 100k\$\Omega\$ may lead to a situation where the input impedance of the ADC changes the measured voltage. Either stick with low value resistors or add a unity-gain buffer between the thermistor and the ADC.

The "5V" provided by a typical board can easily vary by \$\pm\$5%. If you are relying on voltage dividers for precise measurements you need to give them a precise voltage to begin with. Consider using a precision voltage regulator rather than either of the 5V sources you've mentioned.