First, the interpretation of $\eta=\frac{\partial\log y}{\partial\log x}$ and $\eta'=\frac{\partial y}{\partial x}$ are different. $\eta$ is the ratio of percent change and $\eta'$ is the ratio of absolute change. But you already know that. The real question is not why we define “elasticity” as a ratio of percent changes rather than absolute changes in economics, because that's how we use the word “elasticity” in everyday life: suppose rubber band A is 10 inches long and can be stretched by 1 inch when force F is applied, and rubber band B is 1 inch long and can be stretched by 0.5 inch when the same force F is applied. We would say rubber band B is more “elastic” than A, because we don't care about absolute change, but relative change when defining “elasticity”.
So I think your question is “why is elasticity $\eta$ more applicable/useful than $\eta'$?” My answer is that $\eta$ is not more useful/applicable/natural. Both $\eta$ and $\eta'$ are useful in different applications.
Take the price elasticity example. At unit price \$1, consumer A would buy 10 apples, and consumer B would buy 5 apples. At unit price \$2, consumer A would buy 6 apples, and consumer B would buy 1 apple. That is, when the price of apples increases by \$1, both consumers will reduce their purchase by 4 apples. For both consumers, $\eta'=\frac{\Delta\text{apples}}{\Delta\text{price}}=4$. This is a useful quantity if what we wanted to know is what happens to the sales of apples if price increased by \$1. But if we wanted to know which consumer would respond more dramatically to the price change, $\eta'$ is not a good measure. Because it seems consumer B is more “sensitive” to the price changes: she would cut her apple consumption by 80%, compared with only 40% reduction of consumer A. So $\eta$ is a better measure of this “sensitivity” or “elasticity” with respect to price changes.
In your demand curve extrapolation example, assuming constant elasticity $\eta$ is probably closer to truth than assuming constant $\eta'$. If you assume constant $\eta'$, the demand curve is a straight line. This effectively means price change from \$1 to \$2 will induce same change in quantity demanded as the price change from \$100 to \$101. But this is not supported by either evidence or common sense. Human brain does not seem to work this way. In this sense, relative changes do seem to be relevant in more economic applications than the absolute changes.