It does matter. An internal structure that acknowledges the external features is more likely to create those features correctly. A software form that follows the software's function also is likely to be simpler, since the external features arise from the internal design rather than being forced on top of the design. A software system whose form does not mirror its function forever will be difficult to debug, will have more bugs, will be difficult to extend and modify, and likely will perform is core functions poorly. Since we cannot see or touch software, it is sometimes difficult to judge whether a software system's form matches its function.
All software has a definite form however.
Consider an accounting system. To a large extent these functions are separate, but there is some overlap among them also. A software system for business accounting had better reflect these logical accounting operations in its internal design. There should be clearly defined parts of the software for purchasing, billing, payroll, etc. There also should be clear overlap in the software where the logical operations overlap.