Programmable sensor signal reference voltage
Consider this maybe: -
MCP23017 absolute maximum ratings say: -


Maximum output current sourced by any output
pin.......................25 mA

If the output pin is set at 5 volts and the input is down at -10 volts then, the maximum current taken is: -
$$\dfrac{\text{15 volts}}{\text{1000 ohms}}$$
This is 15 mA.
MCP23017 absolute maximum ratings also say: -


Maximum current into VDD pin
.......................................125 mA

So the chip can support 125/15 ADC inputs in this state = 8 ADC lines
If the pull up resistor can be larger in value you'll get more pins available.


Could I use a similar approach, but instead use the MCP23017 pin (as
an output) to turn on/off a transistor? If so, would an n-type MOSFET
be the best option?

Yes you could and a P-channel MOSFET would be your best option because it will pull-up the resistor to the positive rail more effectively and simply than an N-channel device.

What considerations need to be made to ensure the circuit is open (so
far as reasonably practicable) for scenario 1 operation?

Well, you might get circa 1 μA leakage through the MOSFET when it is disabled and this might be a problem.


Are there any other considerations from a protection perspective,
allowing for bipolar inputs which are greater than 5V? I.e. the
circuit should not be at risk if a -~20V signal is connected with the
transistor in either the on or off state.

Here's where you are going hit problems with either a MOSFET or the MCP23017. For the MOSFET there is the reverse diode and this will cause the input to clamp (via the 1 kohm resistor) to Vdd as soon as the input rises above around 5.7 volts and this will load the input line and possibly make accurate ADC measurements unlikely.
The only mechanisms that I think can over come this are: -

Manually applied wire links for those inputs that require a 1 kohm pull-up
Use a relay
Use a solid-state-relay