Weird behaviour of the ADC of an AVR

I don't see any problem with applying an external voltage, through a 5 kohm resistor, to the Arduino reference input. Or better, with using a resistor divider, so that you turn 5 V into your desired AREF voltage, while at the same time exhibiting a source resistance of approximately 5 kohm. This second requirement does not have to be accurate. That is just to limit the current that will flow from AVCC to ground, through the external circuitry.

If you want to end up with 1.8 V at the AREF input of the MCU, just choose R1 and R2 so that \$ V_{AREF} = 5·\frac{R2||32000}{R1+(R2||32000)} =\$ 1.8 V and \$ R_{source} = R1||R2 \approx\$ 5 kohm.

When you need to work with the [0, 1.8] V range, disable the references internal to the ATMega, and when you need to work with the [0, 5] V, enable the internal AVCC reference (if that is 5 V). If the MOSFET shown in Fig. 24-1 (that connects the internal references to the AREF line) has an on resistance much lower than 5 kohm (which I suppose it has), the internal circuitry will see AVCC. In this second situation, the current drain from the internal AVCC (assumed 5 V) to your external resistor divider will be \$\leqslant\$ 1 mA, but that is not a problem.

In summary: it would be bad advice if something could get damaged, but 1 mA won't damage anything.

See Protection of ADC inputs

The simplest form of protection is a Zener diode of suitable voltage across the input. Overvoltage will flow through the zener not your IC. This is a form of "clamp" circuit. Series resistors are added to limit the total current flow into the pin or protection diodes, although those aren't suitable for high frequency applications.