As a preliminary matter, for easy distance days, a goal of 65-80% of max heart rate is effective for aerobic conditioning. But aside from the cardiovascular benefits, you are also seeking other adaptations from long runs as I noted above - strengthening muscles and connective tissue, burning through glycogen from various sources, releasing various hormones at different stages throughout the run (I am a little iffy on that last one). So the time spent at your goal heart rate is a smaller part of the equation when we are talking about a long run compared to a vo2max workout.
Moreover, even on the cardiovascular side, we can do some simple math and see the difference. Take a 16:40 5k runner who is doing 5 x 1000 @ 5k pace with 3:00 rest. It will take that athlete close 2 minutes to get to max heart rate for the first 1000. If he jogs for recovery, it may take only 1:00 to get back to his max heart rate in each subsequent interval. So of the time he is running, he would be at his max heart rate for 10:40. Now consider if he stood around for his recovery periods. Even if it only takes him 1:30 instead of the full 2:00 to get back to his max heart rate in each subsequent interval, you are down to 8:40 at max heart rate instead of 10:40, which is a nearly 20% loss of time at the desired heart rate.
Now compare that to someone out for a 90 minute run. First off, the amount of time that it takes to get to 65% of your max heart rate is negligible - maybe 30 seconds, probably less. For most of us, just standing up from a seated position will get us close to that. Lets say the runner takes 3 breaks to make the math easier. In that case, the runner is still a the desired heart rate for 88 of 90 minutes, losing only 2-3% of the time at the desired heart rate.
And again, being in the desired heart rate range is a much smaller part of the overall value of a long run than it is in a vo2max workout in the first place.