These two phrases both are "comments" on the special trait of something or somebody. The difference lies in that the former is a plain, standalone, comment on a single object, and the latter is an emphatic comment on a single object among many (implies comparison).
For example, a 6' tall girl in a room full of 5' tall girls, you will point at her and say to your companion: "那個女孩,(她)非常高" (那個女孩 = 她). You can also say "她是非常高的" with "在這些女孩中(among the girls)" as the hidden message (在這些女孩中,她是非常高的).
When the same girl passes you on the street, you can repeat the former comment "她非常高", but here, the latter phase - "她是非常高的" does not sound right, unless rephrase it as "在人群中,她是非常高的", with 是非常(很)...的 emphasizing the special trait (高) of her.