My reasoning, which is really Daniels' reasoning, is that you simply do not get your heart rate up to the desired zone for long enough with these shorter intervals. The primary goal of most 5k paced intervals is to improve vo2max. To do that, you need to be training at or close to your max heart rate. According to the studies that Daniels has performed, it takes most trained athletes at least 2 minutes to get up to your max heart rate. As a result, if you are doing 400m intervals, you may not get up to your max heart rate at all. Now you will note that I say "may not." I say this because if you keep the rest really short and make it active rest (jogging), your heart rate will stay elevated between intervals and, after enough intervals, you may be able to get up to your max heart rate at some point in the workout. Same thing is true with 800s.
Let's take a 15:30 5k runner as an example. Let's look at 3 different workouts (and for simplicity's sake, I will assume 5k pace is 5:00 pace):
6 x 800 at 5k pace with 2:00 rest. This is a staple workout that you see folks posting all of the time. Now let's assume that Daniels is right and it takes 2:00 to get up to your max heart rate. At 2:30 per 800, you get 6 periods of 30 seconds each at your max heart rate, tops. Total time at max heart rate: 3:00.
4 x 1200 at 5k pace with 3:00 rest. Another staple workout, with the same total volume of work at 5k pace. In this case though, the athlete will spend 1:45 per interval at their max heart rate, for a total of 7:00 at their max heart rate.
More than twice the time at your max heart rate over the course of the same 4800m at 5k pace by doing 4 1200s instead of 6 800s.
3 x 1600 with 4:00 rest. Total time at max heart rate: 9:00.
Again, you can try to trim some of this deficit when doing 800s by keeping your heart rate up by way of keeping the rest short (cut it down to 1:00 maybe) and by keeping the pace decent on your recovery (7:00 easy distance pace instead of 8:00 jogging pace), but then that becomes a much more intense and higher stress workout.
I am not totally crapping on 400s or 800s at 5k pace. They have their place in the workout cycle. I just think their place is very limited and that they are more suitable for getting you back into things or getting you some work at race pace than they are at actually improving your fitness.