Arduino protecting analog input with internal voltage reference
Yes, it is safe.  The reference voltage is only used as a comparison. The ADC is still powered by, and limited by, the chip's supply voltage (5V).

The AREF voltage has no bearing on what limits there are on voltages you can apply to a pin. All that will happen is that voltages above 1.1V will register as 1023. You can go right up to 5V safely.