With respect, you are misinterpreting him.
If you re-read the sections on VO2 max training (3k or 5k pace) you'll see that it's quite clearly explained why training faster than max VO2 for long intervals can be counter-productive. Specifically, most people don't need to train at 3k pace because they can achieve the same effect at 5k pace. In Daniels' view, it is probably better to do more or longer repeats at 5k pace than a smaller number at 3k pace.
Training at 1500/mile pace has a clear place in Daniels' system, for neuromuscular efficiency and anaerobic capacity. This pace is what he refers to a R pace.
There's also a clear explanation of why preparing to race above and below your target distance is beneficial.
You're right that Daniels does question the value of 3k pace (too slow to be repeats, too quick for intervals) and 10k pace (too slow for intervals, too quick for tempo). Given that (1) those are popular distances to race, and (2) specificity of training should require some work at [realistic] goal pace, there's a question about how to incorporate those into a Daniels' influenced training program. I think it's relatively simple. Say you have 12 sessions of intervals (4k-5k pace) over the season. Substitute some 800s at 3km pace for 1000s at 5k pace in 2-4 workouts. Or substitute 1600-2000m at 10k pace for 1200-1600m intervals at 5k pace. The overall burden of the workout should remain about the same.
Working at goal race pace is a good opportunity to practice hitting splits evenly. If you want to run 9:00 for 3km, you want to practice hitting every 100m in 18 seconds, not running 16, 18, 19, 19 for your first 400m.