The question was really: is it possible to have 2.1 sound from analog source (chromecast audio mainly) unaltered by the amplifier?
I am not sure what you meant by "unaltered by the amplifier"? For now, I would just take a guess and response as follow.
I re-read your original post and noted that you asked "When listening to music, the AVR would be used as a preamp / source selector and send the signal to 2 power amp: one for the speakers, the other one for the sub. "
So if I understood correctly, you would be using a passive subwoofer. In that case, if by 2.1, you mean the source content has the .1, that is the LFE channel then you need to use the sub out for the power amp that drives the passive subwoofer.
If the content is a 2 channel stereo signal then it is not really 2.1 as the .1 wouldn't be discrete and the sub would be playing the same content but the frequency range it gets would be determined by the crossover setting. Also, in that case if you don't want to use the subout, you can just use a Y-splitter to feed both the mains and the subwoofer power amps.
Not sure about Yamaha, but the Denon and Marantz avrs have a 2 channel playback setting too, just take a look of the owner's manuals for details. In that part of the settings, you can choose to have the subwoofer on or not when in direct or pure direct mode.
Those AVRs launched after 2017 (not sure about 2016) are compatible with the $20 App that give you the flexibility to choose the frequency range covered by Audyssey, disabling MRC, customizing target curve etc. In my experience, you get quicker and better results in terms of room correction and smoother bass response than doing it manually, better than using dsp such as the mindsp unless you are an expert in doing it manually with the help of external dsp devices.