Why would there be more adaptation to something that occurs rarely than to something that occurs often?

You appear to be describing the following sort of situation:

BEFORE: 100 units of energy expended / day, of which 70 are the rest requirement and 30 go to discretionary activity. This means that 100 units of energy are consumed per day.

THE CHANGE: discretionary activity increases 20%, leading to 106 units of energy expended / day and food intake of 106 units of metabolizable energy / day.

AFTER: discretionary activity stays constant, but "metabolic adaptation" kicks in, reducing energy expenditure back to 100 units / day. Or, "metabolic adaptation" kicks in, causing a diet that had provided 100 units of energy per day before to provide 106 units / day after.

This doesn't happen, and metabolism is not capable of "adapting" in either of those ways. It is capable of adapting by burning more or less mass per unit time, but you can't burn what isn't there. A person's physical structure may change, which changes the efficiency of various activities (though see below!), and their basal metabolic rate, but that is not a metabolic phenomenon. An elevated level of energy expenditure means an elevated level of food intake.

I have found the paper I assume you're talking about, http://journals.plos.org/plosone/article?id=10.1371/journal.... "Hunter-Gatherer Energetics and Human Obesity". First I'll note that it does not investigate, or discuss, caloric intake at all. Fortunately, we know that for a person who is not gaining or losing weight, caloric intake is equal to energy expenditure. It documents that the Hadza, a group of hunter-gatherers in Tanzania, have the same daily total energy expenditure as other populations elsewhere in the world, except farmers (who have higher energy expenditure). It specifically documents that the energy cost of walking is the same for the Hadza as it is for everyone else:

> comparisons of activities common across cultures do not indicate that Hadza muscle and locomotor physiology [are] inherently more efficient. The energy cost of walking (kCal kg^{−1} m^{−1}) for Hadza adults was well within the range of values reported for Western subjects: of 20 U.S and European populations included in a recent meta-analysis of treadmill walking cost, 14 had mean [minimum cost of travel] values below the Hadza mean. [Resting metabolic rate] for Hadza adults measured while sitting averaged 11% above predicted BMR, within the range of values (7–35%) reported for other populations.

It documents that the Hadza have much higher physical activity levels than Westerners. Since physical activity is just as energetically costly to them as it is to us, this requires that their basal metabolic rate be much lower than ours, and it is -- because they are much smaller than we are:

> Regressing [total energy expenditure] on estimated [basal metabolic rate] suggests that group differences in [physical activity level] were related to differences in body size, as the Hadza are significantly smaller than their Western counterparts. In a multivariate analysis controlling for age and sex, the relationship between TEE and estimated BMR did not differ between Hadza and Western subjects. However, because TEE is correlated with estimated BMR with a slope <1.0, PAL (the ratio of TEE/BMR) tends to be greater among smaller individuals; this is particularly evident among men in our sample.

It documents that traveling, being pregnant, and lactating are all uncorrelated with daily energy expenditures, despite being very energetically expensive. Given this, it speculates:

> We hypothesize that [total energy expenditure] may be a relatively stable, constrained physiological trait for the human species, more a product of our common genetic inheritance than our diverse lifestyles.

This means that when Hadza have to do extra work, they overwhelmingly pay for it by doing less elsewhere rather than eating more. That means that the cost of traveling is actually much higher than it would appear just by looking at the energy requirements -- eating extra food is easy, but empirically you are much more likely to pay for traveling by failing to accomplish things that you otherwise would have done. I don't find that reassuring.

IN SUMMARY:

- Hunter-gatherers meet the high energy requirements of their lifestyle by being physically small, which lowers their basal metabolic rate. This strategy is not open to someone deciding whether to walk or drive; they are already the size they are.

- Hunter-gatherers are no more efficient at walking than anyone else, regardless of your several previous comments. No amount of habituation will lower the energy cost of walking (or running, etc.).

- Empirically, energy you spend on running is likely to be made up by failing to do something else that you would otherwise have done. This cost, where it applies, is probably significantly higher than the energy cost. (On the other hand, this result is from a group of hunter-gatherers who aren't necessarily able to eat additional food even if they'd like to.)