I think you are overestimating the time it takes the average runner to get to 98% of their max heart rate.
I went back and looked at my heart rate data. First, let's recognize a few facts. I use a optical heart rate monitor integrated into my watch which is imperfect, but which is consistent with the heart rate monitor integrated into the elliptical machine I cross train on at the gym, so I think we can consider it accurate enough for our purposes. Second, I do not know my max heart rate as I have never had it lab tested, but based on workouts I have done and a sense of perceived effort developed over the course of more than 25 years in the sport, I can confidently say that the 220-46=174 estimate is a pretty good estimate of my max hear rate - the highest sustained heart rate that I have hit was 180 and I am most often at around 174-178 at peak efforts.
So let's use 176 as my max heart rate and say that my target heart rate range for vo2max workouts is 172 (roughly 98% of 178) to 176. In my two most recent vo2max style workouts, it took between 1:30 and 1:45 per interval to get to my max heart rate. If that is at all representative of the average runner, and based on what Daniels says, it seems to be, then for someone doing 1200m vo2max intervals at 5:20 pace would get more like 2:30 to 2:45 per 1200m/4:00 at their max hear rate.
In addition, you say that it is silly to try to target only one area of improvement during a workout, while also saying that you are never just working one component of physiology when you do a workout. First, I think that your first statement either mischaracterizes, or is a demonstration of a lack of understanding, of this style of training. I would submit that doing vo2max workouts has the primary purpose of improving vo2max, but that it also has secondary benefits with respect to running economy and lactate threshold. They are referred to as vo2max intervals because that is the primary purpose of the workout, not because that is the sole system benefitted by such a workout.
Finally, no workout should be viewed in isolation. You say that isolating physiological factors is silly, and I don't wholly disagree with you on that. Were you to do one style of workout over and over again, you could not expect much improvement after a certain point, and you would not be a well rounded runner nor would you perform up to your underling ability,.
I will say, however, that if you craft a well thought through training program, including workouts within that overall training plan that emphasize one particular physiological factor is a perfectly valid and reasonable (although not the only) way to train. Different systems can be emphasized at different phases of the overall cycle and on different days within each microcycle, and the gains from earlier cycles can be maintained by way of the secondary benefits of workouts emphasizing different factors later in the phase, or through occasional maintenance work within subsequent phases.
That leaves the question of whether the emphasis on just a limited number of specific factors is in itself an appropriate way to train, but I have already gone on way too long on this point, and that is a somewhat separate issue.