The GenerateID table should not be versioned, even if the feature classes it populates are versioned. Attribute Assistant is still able to use and increment the ID values in the non-versioned GenerateID table during a versioned edit session. A single user can also do field calculations on non versioned feature classes or tables during a versioned edit session, but they have to switch to a non-versioned edit session to manually type values into a non-versioned feature class or table.
Because the GenerateID table is non-versioned it restricts that table to being a single user table during edits. Since only one user can update the table at a time and non-versioned edits are done quickly by Attribute Assistant, only one versioned user can gain control of the table at a time to read and update the ID value, which allows Attribute Assistant to avoid duplicates.