@DopeyBadger, thank you again for your thorough response (as always)!
I have noticed this as well. When I was younger, I think I better matched the predicted times with the various running calculators. I think my older body self doesn't seem to agree with these calculators, but I also think that training differently for the longer distances will likely make a difference. In the past, I have used a modified Hal Higdon plan (modified to include Dr. Jack Daniels' threshold, VO2 max, rep workouts) for half marathon and marathon plans, but I feel that there are some downsides to these plans, many of which are points that you mentioned: mainly, barely any miles at/near planned pace (Dr. Jack Daniels), oftentimes too many weekly miles at speed (threshold, VO2 max & reps), and long runs that are a high % of weekly mileage.