> I keep wondering why.

Mainly because the distinction you are making doesn't actually exist.

An apple doesn't "lose" anything by being stored. There are no preservatives, just refrigeration. The apple will proceed to go bad just as quickly once taken out of storage, and it will be just as nutritious as if you had eaten that same apple fresh off the tree.

You can also take that same apple that's been in storage for a year, press the juice out of it, put a culture in it, and it too will grow and be filled with living cultures. The year-stored apple is no less "living" than the milk that you also had to inoculate to turn to yogurt.

In fact, the list of edible things that will not be filled with living cultures, hours after you add a culture to them and then keep them warm for 10 hours, is very short.