Does splitting long endurance rides really affect the training effect of the rides?
"Long" is subjective but those aren't really endurance training sessions. The 30 minute sessions could be completed on glycogen stores alone, and at least the 90 minute sessions after a decent breakfast. One way of thinking of endurance rides (events if you're thinking tri) is those where fuelling during the ride becomes important. 

But there's a massive gap between general fitness advice for the unfit, as you've linked at the end, and training for competition or other challenges, as you've linked earlier. To me you've described athlete A's habit (or even commute) , and athlete B's training plan, as you say the pace is the same and an endurance pace.