The main change that I see in repeated seed saving is that the plants have a stronger internal rhythm. If you sow them in a certain phase, they either jump out of the earth within the phase (sometimes in a matter of the first night) or they wait for the same attribute to appear 9-11 days later. I see them acting as a cohort. Bought seeds are often working pretty random in the first generation and appearing singled out over a period of time.

The biggest difference I think I see in interaction with soil microbes between modern breeds that are adapted to high soil fluid salt content/nitrate consumption and those that are not – conventional or not. I have never tested this by numbers, but it is a gut feeling that has accumulated over the many many variety trials.