ldapdiff combines "diff" and "patch" functionality in one application. The difference is, that ldapdiff is not designed for use on flat ascii files, it is designed for "patching" ldap directories using ldif files.
Normally the primary instance which stores most of a company's data, is a relational database. Since there are normally no ldap servers available, which request their information directly from a relational database, it is difficult, to keep a ldap directory up to date. One could create "ldif formatted deltas" for every database change, but it is time consuming and difficult. With no access to the database application and schema, it is nearly impossible.
Much easier is it, to implement a procedure, which dumps the whole data pool into a ldif formatted file and run ldapdiff.
With ldapdiff it is possible to check every entry/attribute of an ldif file against a running ldap directory. ldapdiff is able to produce ldif delta files, which can be fed, into standard tools like "ldapmodify", "ldapdelete" etc. ldapdiff is also able to modify, delete and add entries/attributes online.

The main idea of ldapdiff, is not to synchronize two different ldap directories. this can be done much better with internal replication tools (e.g. slurpd). ldapdiff's main operational domain are updates of user, groups etc.organized in ldap "ou" branches.