What to call a deficiency that is not inherent?

The word "acquired" has a positive connotation; for example, we acquire skills, not disabilities. The word "unnatural" has irrelevant connotations too.

This is the fundamental flaw in your question. MedicineNet gives the medical definition of acquired as:

Not inherited, or present at birth (congenital), but developing after birth.

This does not imply that all acquired traits are "positive" or "beneficial". There is "acquired immunodeficiency syndrome" (AIDS), and this page lists 10 more diseases that are considered to fall into this category, including Lyme disease, hep C, and the flu. Even the "common cold" is acquired.

So the word you're looking for is acquired.

Since eyesight is variable, due to the shape of the eyeball, it is not really the case that many of the variations are 'deficiencies', anymore than differences in stature are a matter of 'deficiency'.

These are 'attributes' not deficiencies, for who made any rules or regulations about how far one is supposed to be able to see or as to how tall one is meant to stand ?

Attribute : quality, character, or characteristic ascribed to someone or something

Merriam-Webster