You mean the code which is labeled on the website as "A
simple password-based encryption utility is available as
a demonstration of the scrypt key derivation function"?
The additional note is definitely helpful; I still think it would be good to put something at the top level which points people in the right direction.
As is, if someone wants to figure out what to do for password hashing, they have no documentation at the top level. The most promising thing to try, main.c, just uses the encryption functions. If they then jump to the definitions, your note is over 50 lines above the declaration of scryptenc_file, well outside of what will normally show up in their editor window. Yeah, they will probably have to scroll up a little to find the definitions of parameters and return values, but it's possible to do that and miss the note.
I know, people should read the whole documentation, but it's probably easier to just point them in the right direction from the start than to convince people to read the full documentation.