The aerobic system, isn't vastly more efficient. That is on of the myths I am trying to debunk. In the old literature, which is still copied into new literature, it says that anaerobic respiration is 18x less efficient than aerobic respiration.
This is wrong. If there are only 2 ATP produced and used by anaerobic respiration, for every 36 available for pyruvate or lactate oxidation(aerobic resprition), it's because that is the proportion available for each, So that is a total of 38 ATP
So where is the inneficiency?
2 ATP are used up in Glycolysis, another 2 are produced and used up anaerobically, and another 36 are available for aerobic respiration. The numbers vary depending on which reactions take place.
There is no inneficiency other than heat production, which is a metabolic inevitablity.
We humans produce a lot of heat regardless of whether we are engaged in high intensity excercise, or resting. Obviously we produce different amounts according to metabolic rate.
We also produce a lot of heat whether we are hot or cold, but the measurements of this heat loss in terms of aerobic/anaerobically derived heat production are almost impossible to measure accurately.
Your other question about going anaerobic is a good one.
Yes, at the end of a 5000m race, you pick up the pace gradually sometime in the last 1000m, then again on the last lap, and then sprint from about 200m out. The rate of anaerobically derived energy increases during each pick up for a few seconds because you are starting to wind it up, and running maybe ten secods quicker for that lap. However, the amount of anaerobically derived energy quickly starts to run out again, as it did at the start of the race, and in the last 100m the amount of aerobically derived energy increases again, until you are at your limit of effort (if you are trying to outkick the other guys) just as you cross the line.
This explains why, you feel terrible with 250m to go, and then when you kick you feel good for a few seconds (if you have a reasonable kick) and then you gradually go back to feeling terrible again as the finish line approaches and you fight the other guys and the rising fatigue.
So you don't "go anaerobic" in the last 1000m or the last lap, you use a subtle mixture of both aerobic and anaerobic, as you do throughout the race, the amount of each varying constanly, having been practising this all of your life to perfect.
I hope that helps. If you are tired from work and running, you might have to read it a few times.