I tested with a project in the way similar to what you had mentioned.
The output was 3.29 V instead of 2.04V. This could be due to routing path taken by the Reference voltage to the non-inverting input terminal of the opamp.
However, when I used a VDAC instead of a internal reference voltage, the output was correct with a gain of 2, as expected.
The routing path selected by Creator can be found out by reading the .cyfitter file.
I tried to modify the project so that the internal routing is changed.
For this, an analog pin was connected to the output of the buffer (voltage follower) connected to the 1.024V reference.
The output of Voltage follower is connected directly to the non-inverting input terminal of the opamp.
In this case, the output voltage is found to be 2.05V and the voltage at input of non-inverting input terminal is 1.024V.
Hence, when the routing is changed the output is as expected.
The snap shot is attached.
I tryed your last idea, I connected the follower directly to the voltage reference and add an analog pin to the follower input and it works!!
Thank you very much!