Cleaner ADC measurements which of these ways is better

It does not wrap up to something good. There are too many things that can go wrong.

The LC filter is for AVCC, not for AREF.

As I wrote, reading a ratiometric sensor is not the same as reading the voltage of a battery.
When, for example, a LDR is used to measure the light, then the LDR + resistor should be powered with the same voltage as AREF. When AREF is open and the default VCC is used as reference, then it makes sense. If you mess with AREF with a RC or RCRC filter, then you should also power the LDR + resistor with that voltage, but that will drop the voltage after the RCRC filter.

A LDO from 3.4 to 3.3 V while its own drop is 100 mV, that can't be right.

An analog temperature sensor depends so much on the reference voltage, that it is very hard to make accurate. Use a digital temperature sensor, for example the DS18B20.

Why don't you want to use the internal voltage reference ?

In my opinion, the 40 mV ripple is not good and you might make it worse with a wonky reference voltage.