Because SBB fares are calculated from station to station whereas "Verkehrsverbund" or "Tarifverbund" fares are calculated on the basis of zones.

Those are two fundamentally different ways of calculating prices.

So, to re-use NotAllThere's example.

The SBB fare from Basel to Bern is the price from Basel SBB station to Bern station. That ticket is valid on any reasonable service by any reasonable route between those two stations.

Equally, the SBB ticket from Liestal to Bern is valid on any reasonable service by any reasonable route between those two stations.

Now if you have an Abo that covers the zones of Basel SBB, Liestal and whatever there is in between, you can travel from any place in those zones to any other place in those zones. You can, for example, travel from Basel SBB to Liestal. Then in Liestal you can catch a train to Bern. If the train you used to come to Liestal continues to Bern you can even hop straight back onto that same train and into the same seat you were in before. Only you have ended one trip and begun the next by putting one foot outside the train. Now, rather then be pedantic and demand you put one foor outside the train, SBB says it is sufficient that the train has stopped and that you could have put one foot outside the train.